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Takashi Kumasaka

Section

International Center for Synchrotron Radiation Innovation Smart

Job title

Professor

Degree

Doctor of Science (Tokyo Institute of Technology)

researchmap

https://researchmap.jp/read0102094

J-GLOBAL ID

200901009356206423

ORCID

https://orcid.org/0000-0001-9289-1557

Researcher ID

D-7428-2018

Research History 10

2026/04 - Present

Tohoku University　International Center for Synchrotron Radiation Innovation Smart Innovation and Technology Transfer Division　Professor
2026/04 - Present

Japan Synchrotron Radiation Research Institute　JASRI NanoTerasu Research Center　Deputy Director
2025/04 - 2026/03

Japan Synchrotron Radiation Research Institute　Diffraction and Scattering Division　Director
2024/04 - 2025/03

Japan Synchrotron Radiation Research Institute　Center for Synchrotron Radiation Research　Director
2022/04 - 2025/03

Japan Synchrotron Radiation Research Institute　Structural Biology Division　Director
2017/04 - 2022/03

Japan Synchrotron Radiation Research Institute　Protein Crystal Analysis Division　Director
2014/04 - 2017/03

Japan Synchrotron Radiation Research Institute (JASRI/SPring-8)　Protein Crystal Analysis Division　Deputy Director
2007 - 2014

Japan Synchrotron Radiation Research Institute (JASRI/SPring-8)　Research and Utilization Division, Structural Biology Group　Group Leader
2002 - 2007

Tokyo Institute of Technology　Graduate School of Bioscience and Biotechnology　Associate Professor
1996 - 2002

RIKEN (The Institute of Physical and Chemical Research)　Structural Biophysics Laboratory　Research Scientist

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Education 3

Tokyo Institute of Technology　Graduate School of Bioscience and Bioengineering

1991/04 - 1996/03
Tokyo Institute of Technology　School of Science

1987/04 - 1991/03
Saitama Prefectural Kawagoe High School

1984/04 - 1987/03

Committee Memberships 5

日本結晶学会　評議員

2023/04 - Present
日本放射光学会　渉外幹事

2021/10 - 2023/09
日本放射光学会　評議員

2021/10 - 2023/09
日本放射光学会　編集委員

2007 - 2009
日本結晶学会　編集委員

2006 - 2009

Professional Memberships 4

Protein Science Society of Japan
The Biophisical Societiy Of Japan
The Japanese Society for Synchrotron Radiation Research
The Crystallographic Society of Japan

Research Interests 6

放射光
X線結晶学
タンパク質構造
Synchrotron Radiation
X-ray Crystallography
Protein Structure

Research Areas 4

Nanotechnology/Materials / Nanobioscience /
Energy / Quantum beam science /
Life sciences / Biophysics /
Life sciences / Structural biochemistry /

Papers 190

KH–R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB

Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Takato Yano

Nature Communications　2025/09/03

DOI： 10.1038/s41467-025-62302-y 　
The crystal structure of the small zinc-finger protein ZifS from Thermus thermophilus HB8

Saki Kurinami, Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Hiroki Okanishi, Yoshikatsu Kanai, Takato Yano, Ryoji Masui

The Journal of Biochemistry　2025/05/29
Publisher: Oxford University Press (OUP)
DOI： 10.1093/jb/mvaf028 　

ISSN： 0021-924X

eISSN： 1756-2651

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Abstract Zinc finger domains are important interaction modules for binding to nucleic acids, proteins, lipids and small molecules. Many small-sized zinc finger proteins are encoded in bacterial genomes, but most of them have not been functionally annotated. We focused on TTHA0897, ZifS, as a small zinc finger protein from the extremely thermophilic eubacterium Thermus thermophilus HB8. In vivo experiments suggested that the cellular function of ZifS is related to the growth transition of T. thermophilus from the lag to the exponential phase under nutritionally limited conditions. In vitro biochemical experiments, including electrophoretic mobility shift assay and pull-down assay, yielded no clues about molecular functions of ZifS. X-ray crystallographic analysis revealed that the dimeric ZifS globally forms a cylinder-like structure, although ZifS dimer has no overall structural similarity to other known zinc finger proteins. The zinc ion-binding manner of ZifS fitted the characteristics of the zinc ribbon fold, which are mostly found in domains from proteins involved in the transcriptional and translational machinery. The crystal structure of ZifS is the first experimental insight into the molecular structure of this protein family, revealing several conserved features that may be functionally relevant.
Beamline Alignment Software BOSS (Beamline Operation Scheduling Software) for structural biology beamlines at SPring-8

Nobuhiro Mizuno, Kazuya Hasegawa, Takuya Masunaga, Go Ueno, Masaki Yamamoto, Takashi Kumasaka

Journal of Physics: Conference Series　3010　(1)　012090-012090　2025/05/01
Publisher: IOP Publishing
DOI： 10.1088/1742-6596/3010/1/012090 　

ISSN： 1742-6588

eISSN： 1742-6596

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Abstract In synchrotron radiation experiments, precise beamline alignment is essential for optimal conditions and high-quality data. However, this process can be complex and time-consuming. To address this, we developed the Beamline Operation Scheduling Software (BOSS), specifically designed for synchrotron radiation facilities. BOSS schedules and executes processes such as beam alignment, axis scanning based on beam intensity, and instrument positioning. It communicates with control servers using various protocols, including raw sockets, web sockets, HTTP requests, SSH, and serial connections. Users can flexibly edit the parameters and sequence of each process through a graphical interface without modifying the source code. This flexibility allows for easy customization to suit different beamlines or handle urgent issues, making BOSS an effective tool for software prototyping. BOSS has automated many beam alignment processes, reducing the required time by approximately half. It supports external execution of tuning tasks via RESTful API and is also used for temporary tuning, device control in plate diffraction measurements, and beam tuning during automated measurements with ZOO.
Beamline automation opens up cutting edges of Macromolecular crystallography

Masaki Yamamoto, Hiroaki Matsuura, Naoki Sakai, Kunio Hirata, Seiki Baba, Nobuhiro Mizuno, Yuki Nakamura, Hironori Murakami, Kazuya Hasegawa, Takashi Kumasaka

Journal of Physics: Conference Series　3010　(1)　012123-012123　2025/05/01
Publisher: IOP Publishing
DOI： 10.1088/1742-6596/3010/1/012123 　

ISSN： 1742-6588

eISSN： 1742-6596

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Abstract Over the last decade, Macromolecular crystallography (MX) has advanced significantly by developing brilliant micro-focus beamlines, highly sensitive and rapid-readout detectors, and sophisticated data collection systems. Automated data collection has made it possible to efficiently collect large amounts of diffraction data from microcrystals, which would be impossible to achieve manually. This has enabled high-resolution structural analysis of ultra-small crystals, efficient screening of compounds, and new MXs for structural dynamics analysis in crystal fields.
Upgrade for non-cryogenic crystallography of MX beamline BL41XU at SPring-8

Seiki Baba, Kazuya Hasegawa, Nobuhiro Mizuno, Hideo Okumura, Naomine Yano, Naoki Sakai, Takashi Kawamura, Takuya Masunaga, Hironori Murakami, Yuki Nakamura, Go Ueno, Tomoki Fukui, Takaki Irie, Masaki Yamamoto, Takashi Kumasaka

Journal of Physics: Conference Series　3010　(1)　012082-012082　2025/05/01
Publisher: IOP Publishing
DOI： 10.1088/1742-6596/3010/1/012082 　

ISSN： 1742-6588

eISSN： 1742-6596

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Abstract SPring-8 BL41XU is an undulator beamline dedicated to macromolecular crystallography and provides two X-ray energy modes with standard (6.5 to 17.5 keV) and high (20.6 to 35.4 keV) energy ranges. BL41XU was formerly designed and used for conventional cryogenic crystallography. However, the MX beamlines of synchrotron facilities have been newly established or recently upgraded for protein structural dynamics. To adopt these studies, i.e. room-temperature and time-resolved crystallography, we have updated BL41XU in the beamline optics, diffractometers and detectors.
Macromolecular crystallography at SPring-8 and SACLA

Masaki Yamamoto, Takashi Kumasaka

Journal of Synchrotron Radiation　2025/03/01

DOI： 10.1107/S1600577525000657 　
dUTP pyrophosphatases from hyperthermophilic eubacterium and archaeon: Structural and functional examinations on the suitability for PCR application. International-journal

Kenji Fukui, Naoyuki Kondo, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Takato Yano

Protein science : a publication of the Protein Society　33　(11)　e5185　2024/11

DOI： 10.1002/pro.5185 　

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Deoxyuridine triphosphate pyrophosphatase (DUT) suppresses incorporation of uracil into genomic DNA during replication. Thermostable DUTs from hyperthermophilic archaea such as Thermococcus pacificus enhance PCR amplification by preventing misincorporation of dUTP generated by spontaneous deamination of dCTP. However, it is necessary to elucidate whether DUTs do not cause dNTP imbalances during PCR by unwanted side activity. Moreover, it has been unknown what structural features define the thermostability of those DUTs. Here, DUT from a hyperthermophilic eubacterium, Aquifex aeolicus (Aa-DUT), was characterized together with those from T. pacificus (Tp-DUT). Aa-DUT was as thermostable as Tp-DUT up to at least 95°C. The crystal structures of the two thermostable enzymes were determined, which revealed that the structures of Aa-DUT and Tp-DUT resembled those of monofunctional and bifunctional DUTs, respectively. Generally, bifunctional DUTs harbor the dCTP deaminase activity in addition to the DUT activity. However, not only Aa-DUT but also Tp-DUT showed poor activity towards dCTP, indicating both enzymes are monofunctional. We further examined eight types of parameters related to thermostability of protein structure and found that the thermostability of Aa-DUT and Tp-DUT might be accomplished by increased numbers of ion pairs on the protein surface. Finally, we verified that Aa-DUT promoted PCR amplification with Pfu DNA polymerase to the same extent as Tp-DUT. Collectively, we conclude that both DUTs from hyperthermophiles maintain the enzymatic activity at high temperatures without consuming dCTP due to the lack of the deaminate activity.
The structure of the rat vitamin B12 transporter TC and its complex with glutathionylcobalamin

Marcel Bokhove, Takashi Kawamura, Hideo Okumura, Sawako Goto, Yoshiaki Kawano, Stefan Werner, Franziska Jarczowski, Victor Klimyuk, Akihiko Saito, Takashi Kumasaka

Journal of Biological Chemistry　107289-107289　2024/05
Publisher: Elsevier BV
DOI： 10.1016/j.jbc.2024.107289 　

ISSN： 0021-9258
Small-molecule RAS/RAF Binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against a Broad Spectrum of RAS-driven Cancers

Fumi Shima, Yoko Yoshikawa, Yoshiteru Makino, Hirokazu Kubota, Takashi Kawamura, Shigeyuki Matsumoto, Hitomi Yuki, Akira Shibaike, Megumi Okamura, Tomoyo Okada, Manabu Horikawa, Kazumasa Horie, Michiyo Koyanagi-Aoi, Takashi Aoi, Tohru Kataoka, Teruki Honma, Takashi Kumasaka, Hiroo Koyama

2024/01/23

DOI： 10.21203/rs.3.rs-3872110/v1 　
Catalytic mechanism of the zinc-dependent MutL endonuclease reaction Peer-reviewed

Kenji Fukui, Tatsuya Yamamoto, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Takato Yano

Life Science Alliance　6　(10)　e202302001-e202302001　2023/07/24
Publisher: Life Science Alliance, LLC
DOI： 10.26508/lsa.202302001 　

eISSN： 2575-1077

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DNA mismatch repair endonuclease MutL binds two zinc ions. However, the endonuclease activity of MutL is drastically enhanced by other divalent metals such as manganese, implying that MutL binds another catalytic metal at some site other than the zinc-binding sites. Here, we solved the crystal structure of the endonuclease domain ofAquifex aeolicusMutL in the manganese- or cadmium-bound form, revealing that these metals compete with zinc at the same sites. Mass spectrometry revealed that the MutL yielded 5′-phosphate and 3′-OH products, which is characteristic of the two-metal-ion mechanism. Crystallographic analyses also showed that the position and flexibility of a highly conserved Arg ofA. aeolicusMutL altered depending on the presence of zinc/manganese or the specific inhibitor cadmium. Site-directed mutagenesis revealed that the Arg was critical for the catalysis. We propose that zinc ion and its binding sites are physiologically of catalytic importance and that the two-metal-ion mechanism works in the reaction, where the Arg plays a catalytic role. Our results also provide a mechanistic insight into the inhibitory effect of a mutagen/carcinogen, cadmium, on MutL.
Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases Peer-reviewed

Yuya Nishida, Sachiko Yanagisawa, Rikuri Morita, Hideki Shigematsu, Kyoko Shinzawa-Itoh, Hitomi Yuki, Satoshi Ogasawara, Ken Shimuta, Takashi Iwamoto, Chisa Nakabayashi, Waka Matsumura, Hisakazu Kato, Chai Gopalasingam, Takemasa Nagao, Tasneem Qaqorh, Yusuke Takahashi, Satoru Yamazaki, Katsumasa Kamiya, Ryuhei Harada, Nobuhiro Mizuno, Hideyuki Takahashi, Yukihiro Akeda, Makoto Ohnishi, Yoshikazu Ishii, Takashi Kumasaka, Takeshi Murata, Kazumasa Muramoto, Takehiko Tosha, Yoshitsugu Shiro, Teruki Honma, Yasuteru Shigeta, Minoru Kubo, Seiji Takashima, Yasunori Shintani

Nature Communications　13　(1)　2022/12/08
Publisher: Springer Science and Business Media LLC
DOI： 10.1038/s41467-022-34771-y 　

ISSN： 2041-1723

eISSN： 2041-1723
Crystal structure of a nucleotide-binding domain of fatty acid kinase FakA from Thermus thermophilus HB8 Peer-reviewed

Maya Nakatani, Shun-ya Nakahara, Kenji Fukui, Momoka Urano, Yuki Fujii, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Hiroki Okanishi, Yoshikatsu Kanai, Takato Yano, Ryoji Masui

Journal of Structural Biology　214　(4)　107904-107904　2022/12
Publisher: Elsevier BV
DOI： 10.1016/j.jsb.2022.107904 　

ISSN： 1047-8477
Structure and biological evaluation of Caenorhabditis elegans CISD-1/mitoNEET, a KLP-17 tail domain homologue, supports attenuation of paraquat-induced oxidative stress through a p38 MAPK-mediated antioxidant defense response Peer-reviewed

Jacob R. Boos, Hanna N. J, rain, Emi Hagiuda, Alex, er T. Taguchi, Kazuya Hasegawa, Bailey L. Fedun, Sarah J. Taylor, Sofhia M. Elad, Sarah E. Faber, Takashi Kumasaka, Toshio Iwasaki, Werner J. Geldenhuys

Advances in Redox Research　6　100048-100048　2022/09
Publisher: Elsevier {BV}
DOI： 10.1016/j.arres.2022.100048 　

ISSN： 2667-1379
Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases International-journal Peer-reviewed

Samuel L. Rose, Seiki Baba, Hideo Okumura, Svetlana V. Antonyuk, Daisuke Sasaki, Tobias M. Hedison, Muralidharan Shanmugam, Derren J. Heyes, Nigel S. Scrutton, Takashi Kumasaka, Takehiko Tosha, Robert R. Eady, Masaki Yamamoto, S. Samar Hasnain

Proceedings of the National Academy of Sciences　119　(30)　e2205664119　2022/07/26

DOI： 10.1073/pnas.2205664119 　

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Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.
In situ crystal data-collection and ligand-screening system at SPring-8 International-journal Peer-reviewed

Hideo Okumura, Naoki Sakai, Hironori Murakami, Nobuhiro Mizuno, Yuki Nakamura, Go Ueno, Takuya Masunaga, Takashi Kawamura, Seiki Baba, Kazuya Hasegawa, Masaki Yamamoto, Takashi Kumasaka

Acta Crystallographica Section F Structural Biology Communications　78　(6)　241-251　2022/06

DOI： 10.1107/s2053230x22005283 　

ISSN： 2053-230X

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In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein-ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.
Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction. International-journal Peer-reviewed

Kenji Fukui, Masao Inoue, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Takato Yano

Structure (London, England : 1993)　30　(7)　973-982　2022/04/08

DOI： 10.1016/j.str.2022.03.014 　

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MutS family proteins are classified into MutS-I and -II lineages: MutS-I recognizes mismatched DNA and initiates mismatch repair, whereas MutS-II recognizes DNA junctions to modulate recombination. MutS-I forms dimeric clamp-like structures enclosing the mismatched DNA, and its composite ATPase sites regulate DNA-binding modes. Meanwhile, the structures of MutS-II have not been determined; accordingly, it remains unknown how MutS-II recognizes DNA junctions and how nucleotides control DNA binding. Here, we solved the ligand-free and ADP-bound crystal structures of bacterial MutS2 belonging to MutS-II. MutS2 also formed a dimeric clamp-like structure with composite ATPase sites. The ADP-bound MutS2 was more flexible compared to the ligand-free form and could be more suitable for DNA entry. The inner hole of the MutS2 clamp was two times larger than that of MutS-I, and site-directed mutagenesis analyses revealed DNA-binding sites at the inner hole. Based on these, a model is proposed that describes how MutS2 recognizes DNA junctions.
Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment Peer-reviewed

Migiwa Takeda, Seiki Baba, Jiro Okuma, Yoshitsugu Hirose, Asuka Nishimura, Masaki Takata, Kohei Oda, Daisuke Shibata, Takashi Kumasaka, Yasuhiro Kondo

Communications Biology　5　(1)　247　2022/03/22
Publisher: Springer Science and Business Media {LLC}
DOI： 10.1038/s42003-022-03195-1 　

ISSN： 2399-3642

eISSN： 2399-3642

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Abstract Enzymatic breakdown is an attractive cellulose utilisation method with a low environmental load. Its high temperature operation could promote saccharification and lower contamination risk. Here we report a hyper-thermostable cellobiohydrolase (CBH), named HmCel6A and its variant HmCel6A-3SNP that were isolated metagenomically from hot spring sediments and expressed in Escherichia coli. They are classified into glycoside hydrolases family 6 (GH6). HmCel6A-3SNP had three amino acid replacements to HmCel6A (P88S/L230F/F414S) and the optimum temperature at 95 °C, while HmCel6A did it at 75 °C. Crystal structure showed conserved features among GH6, a (β/α)₈-barrel core and catalytic residues, and resembles TfCel6B, a bacterial CBH II of Thermobifida fusca, that had optimum temperature at 60 °C. From structure-function studies, we discuss unique structural features that allow the enzyme to reach its high thermostability level, such as abundance of hydrophobic and charge-charge interactions, characteristic metal bindings and disulphide bonds. Moreover, structure and surface plasmon resonance analysis with oligosaccharides suggested that the contribution of an additional tryptophan located at the tunnel entrance could aid in substrate recognition and thermostability. These results may help to design efficient enzymes and saccharification methods for cellulose working at high temperatures.
Radiation-induced defects in protein crystals observed by X-ray topography Peer-reviewed

Ryo Suzuki, Seiki Baba, Nobuhiro Mizuno, Kazuya Hasegawa, Haruhiko Koizumi, Kenichi Kojima, Takashi Kumasaka, Masaru Tachibana

Acta Crystallographica Section D Structural Biology　78　(2)　196-203　2022/02/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S205979832101281X 　

ISSN： 2059-7983

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The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.
Guidelines for de novo phasing using multiple small-wedge data collection Peer-reviewed

Seiki Baba, Hiroaki Matsuura, Takashi Kawamura, Naoki Sakai, Yuki Nakamura, Yoshiaki Kawano, Nobuhiro Mizuno, Takashi Kumasaka, Masaki Yamamoto, Kunio Hirata

Journal of Synchrotron Radiation　28　(5)　1284-1295　2021/09/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S1600577521008067 　

ISSN： 1600-5775

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Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5–20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for <italic>de novo</italic> structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.
Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein International-journal Peer-reviewed

Shigeyuki Matsumoto, Haruka Taniguchi-Tamura, Mitsugu Araki, Takashi Kawamura, Ryo Miyamoto, Chiemi Tsuda, Fumi Shima, Takashi Kumasaka, Yasushi Okuno, Tohru Kataoka

Biochemical and Biophysical Research Communications　565　85-90　2021/08
Publisher: Elsevier {BV}
DOI： 10.1016/j.bbrc.2021.05.084 　

ISSN： 0006-291X

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GTP-bound forms of Ras proteins (Ras•GTP) assume two interconverting conformations, "inactive" state 1 and "active" state 2. Our previous study on the crystal structure of the state 1 conformation of H-Ras in complex with guanosine 5'-(β, γ-imido)triphosphate (GppNHp) indicated that state 1 is stabilized by intramolecular hydrogen-bonding interactions formed by Gln61. Since Ras are constitutively activated by substitution mutations of Gln61, here we determine crystal structures of the state 1 conformation of H-Ras•GppNHp carrying representative mutations Q61L and Q61H to observe the effect of the mutations. The results show that these mutations alter the mode of hydrogen-bonding interactions of the residue 61 with Switch II residues and induce conformational destabilization of the neighboring regions. In particular, Q61L mutation results in acquirement of state 2-like structural features. Moreover, the mutations are likely to impair an intramolecular structural communication between Switch I and Switch II. Molecular dynamics simulations starting from these structures support the above observations. These findings may give a new insight into the molecular mechanism underlying the aberrant activation of the Gln61 mutants.
Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography Peer-reviewed

Takashi Nomura, Tetsunari Kimura, Yusuke Kanematsu, Daichi Yamada, Keitaro Yamashita, Kunio Hirata, Go Ueno, Hironori Murakami, Tamao Hisano, Raika Yamagiwa, Hanae Takeda, Chai Gopalasingam, Ryota Kousaka, Sachiko Yanagisawa, Osami Shoji, Takashi Kumasaka, Masaki Yamamoto, Yu Takano, Hiroshi Sugimoto, Takehiko Tosha, Minoru Kubo, Yoshitsugu Shiro

Proceedings of the National Academy of Sciences　118　(21)　e2101481118-e2101481118　2021/05/25
Publisher: Proceedings of the National Academy of Sciences
DOI： 10.1073/pnas.2101481118 　

ISSN： 1091-6490

eISSN： 1091-6490

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<jats:p>Nitric oxide (NO) reductase from the fungus <jats:italic>Fusarium oxysporum</jats:italic> is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N<jats:sub>2</jats:sub>O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate (<jats:italic><jats:underline>I</jats:underline></jats:italic>), a key state to promote N–N bond formation and N–O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of <jats:italic><jats:underline>I</jats:underline></jats:italic>. TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe–NO coordination in <jats:italic><jats:underline>I</jats:underline></jats:italic>, with an elongated Fe–NO bond length (Fe–NO = 1.91 Å, Fe–N–O = 138°) in the absence of NAD<jats:sup>+</jats:sup>. TR-infrared (IR) spectroscopy detects the formation of <jats:italic><jats:underline>I</jats:underline></jats:italic> with an N–O stretching frequency of 1,290 cm<jats:sup>−1</jats:sup> upon hydride transfer from NADH to the Fe<jats:sup>3+</jats:sup>–NO enzyme via the dissociation of NAD<jats:sup>+</jats:sup> from a transient state, with an N–O stretching of 1,330 cm<jats:sup>−1</jats:sup> and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of <jats:italic><jats:underline>I</jats:underline></jats:italic> is characterized by a singly protonated Fe<jats:sup>3+</jats:sup>–NHO<jats:sup>•−</jats:sup> radical. The current findings provide conclusive evidence for the N<jats:sub>2</jats:sub>O generation mechanism via a radical–radical coupling of the heme nitroxyl complex with the second NO molecule.</jats:p>
Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method Peer-reviewed

Kazuya Hasegawa, Seiki Baba, Takashi Kawamura, Masaki Yamamoto, Takashi Kumasaka

Acta Crystallographica Section D Structural Biology　77　(3)　300-312　2021/03/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S2059798321001686 　

ISSN： 2059-7983

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Synchrotron serial crystallography (SSX) is an emerging data-collection method for micro-crystallography on synchrotron macromolecular (MX) crystallography beamlines. At SPring-8, the feasibility of the fixed-target approach was examined by collecting data using a 2D raster scan combined with goniometer rotation. Results at cryogenic temperatures demonstrated that rotation is effective for efficient data collection in SSX and the method was named serial synchrotron rotation crystallography (SS-ROX). To use this method for room-temperature (RT) data collection, a humid air and glue-coating (HAG) method was developed in which data were collected from polyvinyl alcohol-coated microcrystals fixed on a loop under humidity-controlled air. The performance and the RT data-collection strategy for micro-crystallography were evaluated using microcrystals of lysozyme. Although a change in unit-cell dimensions of up to 1% was observed during data collection, the impact on data quality was marginal. A comparison of data obtained at various absorbed doses revealed that absorbed doses of up to 210 kGy were tolerable in both global and local damage. Although this limits the number of photons deposited on each crystal, increasing the number of merged images improved the resolution. On the basis of these results, an equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.
Erratum: Guidelines for de novo phasing using multiple small-wedge data collection.(Journal of Synchrotron Radiation (2021) 28 (1284–1295) DOI: 10.1107/S1600577521008067)

Baba, S., Matsuura, H., Kawamura, T., Sakai, N., Nakamura, Y., Kawano, Y., Mizuno, N., Kumasaka, T., Yamamoto, M., Hirata, K.

Journal of Synchrotron Radiation　29　(2)　593-593　2021
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S1600577522001655 　

ISSN： 1600-5775 0909-0495
Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals Peer-reviewed

Yuki Nakamura, Seiki Baba, Nobuhiro Mizuno, Takaki Irie, Go Ueno, Kunio Hirata, Sho Ito, Kazuya Hasegawa, Masaki Yamamoto, Takashi Kumasaka

Acta Crystallographica Section F Structural Biology Communications　76　(12)　616-622　2020/12/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S2053230X2001420X 　

eISSN： 2053-230X

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Cryocrystallography is a technique that is used more often than room-temperature data collection in macromolecular crystallography. One of its advantages is the significant reduction in radiation damage, which is especially useful in synchrotron experiments. Another advantage is that cryopreservation provides simple storage of crystals and easy transportation to a synchrotron. However, this technique sometimes results in the undesirable adhesion of frost to mounted crystals. The frost produces noisy diffraction images and reduces the optical visibility of crystals, which is crucial for aligning the crystal position with the incident X-ray position. To resolve these issues, a computer-controlled device has been developed that drizzles liquid nitrogen over a crystal to remove frost. It was confirmed that the device works properly, reduces noise from ice rings in diffraction images and enables the centering of crystals with low visibility owing to frost adhesion.
A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL. International-journal Peer-reviewed

Keisuke Izuhara, Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Kazuhisa Uchiyama, Takato Yano

The Journal of biological chemistry　295　(33)　11643-11655　2020/06/22

DOI： 10.1074/jbc.RA120.013576 　

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In humans, mutations in genes encoding homologs of the DNA mismatch repair endonuclease MutL cause a hereditary cancer that is known as Lynch syndrome. Here, we determined the crystal structures of the N-terminal domain (NTD) of MutL from the thermophilic eubacterium Aquifex aeolicus (aqMutL) complexed with ATP analogs at 1.69-1.73 Å. The structures revealed significant structural similarities to those of a human MutL homolog, Postmeiotic segregation increased 2 (PMS2). We introduced five Lynch syndrome-associated mutations clinically found in human PMS2 into the aqMutL NTD and investigated the protein stability, ATPase activity, and DNA-binding ability of these protein variants. Among the mutations studied, the most unexpected results were obtained for the residue Ser34. Ser34 (Ser46 in PMS2) is located at a previously-identified Bergerat ATP-binding fold. We found that the S34I aqMutL NTD retains ATPase and DNA-binding activities. Interestingly, CD spectrometry and trypsin limited proteolysis indicated disruption of a secondary structure element of the S34I NTD, destabilizing the overall structure of the aqMutL NTD. In agreement with this, the recombinant human PMS2 S46I NTD was easily digested in the host Escherichia coli cells. Moreover, other mutations resulted in reduced DNA-binding or ATPase activity. In summary, using the thermostable aqMutL protein as a model molecule, we have experimentally determined the effects of the mutations on MutL endonuclease; we discuss the pathological effects of the corresponding mutations in human PMS2.
X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii. International-journal Peer-reviewed

Yusuke Ohnishi, Norifumi Muraki, Daiki Kiyota, Hideo Okumura, Seiki Baba, Yoshiaki Kawano, Takashi Kumasaka, Hideaki Tanaka, Genji Kurisu

Journal of biochemistry　167　(6)　549-555　2020/06/01

DOI： 10.1093/jb/mvaa045 　

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Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported so far, very likely a given number of them was partially reduced by strong X-ray. To understand the precise structural change between reduced and oxidized Fd, it is important to know whether the crystals of oxidized Fd may or may not be reduced during the X-ray experiment. We prepared the thin plate-shaped Fd crystals from Chlamydomonas reinhardtii and monitored its absorption spectra during experiment. Absorption spectra of oxidized Fd crystals were clearly changed to that of reduced form in an X-ray dose-dependent manner. In another independent experiment, the X-ray diffraction images obtained from different parts of one single crystal were sorted and merged to form two datasets with low and high X-ray doses. An Fo-Fo map calculated from the two datasets showed that X-ray reduction causes a small displacement of the iron atoms in the [2Fe-2S] cluster. Both our spectroscopic and crystallographic studies confirm X-ray dose-dependent reduction of Fd, and suggest a structural basis for its initial reduction step especially in the core of the cluster.
Development of SPACE-II for rapid sample exchange at SPring-8 macromolecular crystallography beamlines Peer-reviewed

Hironori Murakami, Kazuya Hasegawa, Go Ueno, Naoto Yagi, Masaki Yamamoto, Takashi Kumasaka

Acta Crystallographica Section D Structural Biology　76　(2)　155-165　2020/02/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S2059798320000030 　
An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser Peer-reviewed

Michihiro Suga, Fusamichi Akita, Keitaro Yamashita, Yoshiki Nakajima, Go Ueno, Hongjie Li, Takahiro Yamane, Kunio Hirata, Yasufumi Umena, Shinichiro Yonekura, Long-Jiang Yu, Hironori Murakami, Takashi Nomura, Tetsunari Kimura, Minoru Kubo, Seiki Baba, Takashi Kumasaka, Kensuke Tono, Makina Yabashi, Hiroshi Isobe, Kizashi Yamaguchi, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen

Science　366　(6463)　334-338　2019/10
Publisher: American Association for the Advancement of Science ({AAAS})
DOI： 10.1126/science.aax6998 　

ISSN： 0036-8075
A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method Peer-reviewed

Seiki Baba, Atsuhiro Shimada, Nobuhiro Mizuno, Junpei Baba, Hideo Ago, Masaki Yamamoto, Takashi Kumasaka

Journal of Applied Crystallography　52　(4)　2019/08/01
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S1600576719006435 　
Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays International-journal Peer-reviewed

Go Ueno, Atsuhiro Shimada, Eiki Yamashita, Kazuya Hasegawa, Takashi Kumasaka, Kyoko Shinzawa-Itoh, Shinya Yoshikawa, Tomitake Tsukihara, Masaki Yamamoto

Journal of Synchrotron Radiation　26　(4)　912-921　2019/07
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/S1600577519006805 　

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To investigate the effect of high-energy X-rays on site-specific radiation-damage, low-dose diffraction data were collected from radiation-sensitive crystals of the metal enzyme cytochrome c oxidase. Data were collected at the Structural Biology I beamline (BL41XU) at SPring-8, using 30 keV X-rays and a highly sensitive pixel array detector equipped with a cadmium telluride sensor. The experimental setup of continuous sample translation using multiple crystals allowed the average diffraction weighted dose per data set to be reduced to 58 kGy, and the resulting data revealed a ligand structure featuring an identical bond length to that in the damage-free structure determined using an X-ray free-electron laser. However, precise analysis of the residual density around the ligand structure refined with the synchrotron data showed the possibility of a small level of specific damage, which might have resulted from the accumulated dose of 58 kGy per data set. Further investigation of the photon-energy dependence of specific damage, as assessed by variations in UV-vis absorption spectra, was conducted using an on-line spectrometer at various energies ranging from 10 to 30 keV. No evidence was found for specific radiation damage being energy dependent.
ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. International-journal Peer-reviewed

Kunio Hirata, Keitaro Yamashita, Go Ueno, Yoshiaki Kawano, Kazuya Hasegawa, Takashi Kumasaka, Masaki Yamamoto

Acta crystallographica. Section D, Structural biology　75　(Pt 2)　138-150　2019/02/01

DOI： 10.1107/S2059798318017795 　

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Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.
In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase. International-journal Peer-reviewed

Takeshi Murakawa, Seiki Baba, Yoshiaki Kawano, Hideyuki Hayashi, Takato Yano, Takashi Kumasaka, Masaki Yamamoto, Katsuyuki Tanizawa, Toshihide Okajima

Proceedings of the National Academy of Sciences of the United States of America　116　(1)　135-140　2019/01/02
Publisher: Proceedings of the National Academy of Sciences
DOI： 10.1073/pnas.1811837116 　

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In the catalytic reaction of copper amine oxidase, the protein-derived redox cofactor topaquinone (TPQ) is reduced by an amine substrate to an aminoresorcinol form (TPQamr), which is in equilibrium with a semiquinone radical (TPQsq). The transition from TPQamr to TPQsq is an endothermic process, accompanied by a significant conformational change of the cofactor. We employed the humid air and glue-coating (HAG) method to capture the equilibrium mixture of TPQamr and TPQsq in noncryocooled crystals of the enzyme from Arthrobacter globiformis and found that the equilibrium shifts more toward TPQsq in crystals than in solution. Thermodynamic analyses of the temperature-dependent equilibrium also revealed that the transition to TPQsq is entropy-driven both in crystals and in solution, giving the thermodynamic parameters that led to experimental determination of the crystal packing effect. Furthermore, we demonstrate that the binding of product aldehyde to the hydrophobic pocket in the active site produces various equilibrium states among two forms of the product Schiff-base, TPQamr, and TPQsq, in a pH-dependent manner. The temperature-controlled HAG method provides a technique for thermodynamic analysis of conformational changes occurring in protein crystals that are hardly scrutinized by conventional cryogenic X-ray crystallography.
Remodeling of the optics for a micro-focusing protein crystallography beamline at SPring-8

Shunji Goto, Tomoyuki Takeuchi, Yasunori Senba, Hirokatsu Yumoto, Hiroshi Yamazaki, Haruhiko Ohashi, Seiki Baba, Nobuhiro Mizuno, Yuki Nakamura, Kazuya Hasegawa, Takashi Kumasaka, Kunio Hirata, Keitaro Yamashita, Naoki Sakai, Masaki Yamamoto

Proceedings of SPIE - The International Society for Optical Engineering　11108　2019

DOI： 10.1117/12.2530667 　

ISSN： 0277-786X

eISSN： 1996-756X
Upgrade of bending magnet MX beamline BL38B1 at SPring-8

Seiki Baba, Nobuhiro Mizuno, Hideo Okumura, Nipawan Nuemket, Kazuya Hasegawa, Yuki Nakamura, Hironori Murakami, Go Ueno, Tomoki Fukui, Takaki Irie, Masayuki Tanaka, Hiroshi Yamazaki, Haruhiko Ohashi, Masaki Yamamoto, Takashi Kumasaka

13TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION (SRI2018)　2054　2019

DOI： 10.1063/1.5084639 　

ISSN： 0094-243X
結晶調湿Ｘ線回折法と室温測定の再評価 Invited Peer-reviewed

熊坂崇, 馬場清喜, 河村高志

日本結晶成長学会誌　45　(4)　2019/01

DOI： 10.19009/jjacg.3-45-4-02 　

ISSN： 2187-8366
Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus Peer-reviewed

Kenji Fukui, Seiki Baba, Takashi Kumasaka, Takato Yano

FEBS Letters　592　(9)　1611-1619　2018/05/01
Publisher: Wiley Blackwell
DOI： 10.1002/1873-3468.13050 　

ISSN： 1873-3468 0014-5793
Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals Peer-reviewed

Ryo Suzuki, Haruhiko Koizumi, Keiichi Hirano, Takashi Kumasaka, Kenichi Kojima, Masaru Tachibana

Proceedings of the National Academy of Sciences of the United States of America　115　(14)　3634-3639　2018/04/03
Publisher: National Academy of Sciences
DOI： 10.1073/pnas.1720098115 　

ISSN： 1091-6490 0027-8424
Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling Peer-reviewed

Alexander T. Taguchi, Yoshiharu Miyajima-Nakano, Risako Fukazawa, Myat T. Lin, Amgalanbaatar Baldansuren, Robert B. Gennis, Kazuya Hasegawa, Takashi Kumasaka, Sergei A. Dikanov, Toshio Iwasaki

Inorganic Chemistry　57　(2)　741-746　2018/01/16
Publisher: American Chemical Society
DOI： 10.1021/acs.inorgchem.7b02676 　

ISSN： 1520-510X 0020-1669
Construction of a supramolecule comprising [2,3,9,10,16,17,23,24-octakis(2,6-dimethylphenoxy)phthalocyaninato]zinc(II) and (5,10,15,20-tetraphenylporphyrinato)zinc(II) Peer-reviewed

Masatomo Makino, Kazuhiko Matsubayashi, Yukiko Kodama-Oda, Naoto Imawaka, Nobuhiro Mizuno, Takashi Kumasaka, Katsumi Yoshino

IUCrData　3　(12)　2018
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/s2414314618017418 　

ISSN： 2414-3146
Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy Peer-reviewed

Shota Matsunaga, Yuta Hano, Yuta Saito, Kazuhiro J. Fujimoto, Takashi Kumasaka, Shigeyuki Matsumoto, Tohru Kataoka, Fumi Shima, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　77　51-63　2017/10

DOI： 10.1016/j.jmgm.2017.07.028 　

ISSN： 1093-3263

eISSN： 1873-4243
Crystallization and X-ray analysis of 23 nm virus-like particles from Norovirus Chiba strain Peer-reviewed

Kazuya Hasegawa, Yuichi Someya, Hideki Shigematsu, Tomomi Kimura-Someya, Nipawan Nuemket, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS　73　(10)　568-573　2017/10

DOI： 10.1107/S2053230X17013759 　

ISSN： 2053-230X
A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate Peer-reviewed

Ai Kaneko, Kasumi Uenishi, Yukie Maruyama, Nobuhiro Mizuno, Seiki Baba, Takashi Kumasaka, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto

JOURNAL OF BIOLOGICAL CHEMISTRY　292　(38)　15681-15690　2017/09

DOI： 10.1074/jbc.M117.793992 　

ISSN： 0021-9258

eISSN： 1083-351X
Protein microcrystallography using synchrotron radiation Peer-reviewed

Masaki Yamamoto, Kunio Hirata, Keitaro Yamashita, Kazuya Hasegawa, Go Ueno, Hideo Ago, Takashi Kumasaka

IUCRJ　4　(5)　529-539　2017/09

DOI： 10.1107/S2052252517008193 　

ISSN： 2052-2525
Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus Peer-reviewed

Kenji Fukui, Hitoshi Iino, Seiki Baba, Takashi Kumasaka, Seiki Kuramitsu, Takato Yano

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS　1865　(9)　1178-1187　2017/09

DOI： 10.1016/j.bbapap.2017.06.024 　

ISSN： 1570-9639

eISSN： 0006-3002
Structural basis for intramolecular interaction of post-translationally modified H-Ras.GTP prepared by protein ligation Peer-reviewed

Haoliang Ke, Shigeyuki Matsumoto, Yosuke Murashima, Haruka Taniguchi-Tamura, Ryo Miyamoto, Yoko Yoshikawa, Chiemi Tsuda, Takashi Kumasaka, Eiichi Mizohata, Hironori Edamatsu, Tohru Kataoka

FEBS LETTERS　591　(16)　2470-2481　2017/08

DOI： 10.1002/1873-3468.12759 　

ISSN： 1873-3468
A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase Peer-reviewed

Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyoko Shinzawa-Itoh, Junpei Baba, Keita Hatano, Yuki Eto, Akari Miyamoto, Hironori Murakami, Takashi Kumasaka, Shigeki Owada, Kensuke Tono, Makina Yabashi, Yoshihiro Yamaguchi, Sachiko Yanagisawa, Miyuki Sakaguchi, Takashi Ogura, Ryo Komiya, Jiwang Yan, Eiki Yamashita, Masaki Yamamoto, Hideo Ago, Shinya Yoshikawa, Tomitake Tsukihara

SCIENCE ADVANCES　3　(7)　e1603042　2017/07

DOI： 10.1126/sciadv.1603042 　

ISSN： 2375-2548
Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus. Peer-reviewed

Fukui K, Iino H, Baba S, Kumasaka T, Kuramitsu S, Yano T

Biochimica et biophysica acta　2017/06

DOI： 10.1016/j.bbapap.2017.06.024 　

ISSN： 0006-3002
Alteration of the alpha(1)beta(2)/alpha(2)beta(1) subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice Peer-reviewed

Noriko Inoguchi, Nobuhiro Mizuno, Seiki Baba, Takashi Kumasaka, Chandrasekhar Natarajan, Jay F. Storz, Hideaki Moriyama

PLOS ONE　12　(3)　e0174921　2017/03

DOI： 10.1371/journal.pone.0174921 　

ISSN： 1932-6203
Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida Peer-reviewed

Yutaka Yorinaga, Takashi Kumasaka, Masaki Yamamoto, Kensaku Hamada, Makoto Kawamukai

FEBS LETTERS　591　(3)　540-547　2017/02

DOI： 10.1002/1873-3468.12557 　

ISSN： 0014-5793

eISSN： 1873-3468
Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b Peer-reviewed

Sivaraman Padavattan, Viswanathan Thiruselvam, Toshie Shinagawa, Kazuya Hasegawa, Takashi Kumasaka, Shunsuke Ishii, Thirumananseri Kumarevel

BIOPHYSICAL CHEMISTRY　221　41-48　2017/02

DOI： 10.1016/j.bpc.2016.11.013 　

ISSN： 0301-4622

eISSN： 1873-4200
Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography Peer-reviewed

Kazuya Hasegawa, Keitaro Yamashita, Tomohiro Murai, Nipawan Nuemket, Kunio Hirata, Go Ueno, Hideo Ago, Toru Nakatsu, Takashi Kumasaka, Masaki Yamamoto

JOURNAL OF SYNCHROTRON RADIATION　24　(1)　29-41　2017/01

DOI： 10.1107/S1600577516016362 　

ISSN： 1600-5775
Self-assembly of tetravalent Goldberg polyhedra from 144 small components Peer-reviewed

Daishi Fujita, Yoshihiro Ueda, Sota Sato, Nobuhiro Mizuno, Takashi Kumasaka, Makoto Fujita

NATURE　540　(7634)　563-+　2016/12

DOI： 10.1038/nature20771 　

ISSN： 0028-0836

eISSN： 1476-4687
Structural Features and Functional Dependency on -Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL Peer-reviewed

Kenji Fukui, Seiki Baba, Takashi Kumasaka, Takato Yano

JOURNAL OF BIOLOGICAL CHEMISTRY　291　(33)　16990-17000　2016/08

DOI： 10.1074/jbc.M116.739664 　

ISSN： 0021-9258

eISSN： 1083-351X
Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii Peer-reviewed

Yuzo Watanabe, Hisaaki Yanai, Mayumi Kanagawa, Sakiko Suzuki, Satoko Tamura, Kiyoshi Okada, Seiki Baba, Takashi Kumasaka, Yoshihiro Agari, Lirong Chen, Zheng-Qing Fu, John Chrzas, Bi-Cheng Wang, Noriko Nakagawa, Akio Ebihara, Ryoji Masui, Seiki Kuramitsu, Shigeyuki Yokoyama, Gen-ichi Sampei, Gota Kawai

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS　72　(8)　627-635　2016/08

DOI： 10.1107/S2053230X1600978X 　

ISSN： 2053-230X
Self-Assembly of M30L60 Icosidodecahedron Peer-reviewed

Daishi Fujita, Yoshihiro Ueda, Sota Sato, Hiroyuki Yokoyama, Nobuhiro Mizuno, Takashi Kumasaka, Makoto Fujita

CHEM　1　(1)　91-101　2016/07

DOI： 10.1016/j.chempr.2016.06.007 　

ISSN： 2451-9294
Molecular Mechanism for Conformational Dynamics of Ras.GTP Elucidated from In-Situ Structural Transition in Crystal Peer-reviewed

Shigeyuki Matsumoto, Nao Miyano, Seiki Baba, Jingling Liao, Takashi Kawamura, Chiemi Tsuda, Azusa Takeda, Masaki Yamamoto, Takashi Kumasaka, Tohru Kataoka, Fumi Shima

SCIENTIFIC REPORTS　6　25931　2016/05

DOI： 10.1038/srep25931 　

ISSN： 2045-2322
Remote access and automation of SPring-8 MX beamlines Peer-reviewed

Go Ueno, Takaaki Hikima, Keitaro Yamashita, Kunio Hirata, Kazuya Hasegawa, Hironori Murakami, Yukito Furukawa, Nobuhiro Mizuno, Takashi Kumasaka, Masaki Yamamoto

PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION (SRI2015)　1741　2016

DOI： 10.1063/1.4952941 　

ISSN： 0094-243X
SPring-8 BL44XU, Beamline Designed for Structure Analysis of Large Biological Macromolecular Assemblies Peer-reviewed

Akifumi Higashiura, Eiki Yamashita, Masato Yoshimura, Kazuya Hasegawa, Yukito Furukawa, Takashi Kumasaka, Go Ueno, Masaki Yamamoto, Tomitake Tsukihara, Atsushi Nakagawa

PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION (SRI2015)　1741　2016

DOI： 10.1063/1.4952851 　

ISSN： 0094-243X
Automated system for data collection and data processing using microcrystals Peer-reviewed

Keitaro Yamashita, Kunio Hirata, Yoshiaki Kawano, Go Ueno, Kazuya Hasegawa, Takashi Kumasaka, Masaki Yamamoto

Acta Crystallographica Section A Foundations and Advances　71　(a1)　s187-s187　2015/08
Publisher: International Union of Crystallography ({IUCr})
DOI： 10.1107/s2053273315097247 　

ISSN： 2053-2733
Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming Peer-reviewed

Sivaraman Padavattan, Toshie Shinagawa, Kazuya Hasegawa, Takashi Kumasaka, Shunsuke Ishii, Thirumananseri Kumarevel

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　464　(3)　929-935　2015/08

DOI： 10.1016/j.bbrc.2015.07.070 　

ISSN： 0006-291X

eISSN： 1090-2104
Structural Basis for Polymer Packing and Solvation Properties of the Organogermanium Crystalline Polymer Propagermanium and Its Derivatives Peer-reviewed

Nobuhiro Mizuno, Eiji Nishibori, Mitsuru Oka, Takahito Jomori, Masaki Takata, Takashi Kumasaka

JOURNAL OF PHARMACEUTICAL SCIENCES　104　(8)　2482-2488　2015/08

DOI： 10.1002/jps.24486 　

ISSN： 0022-3549

eISSN： 1520-6017
Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis Peer-reviewed

Aik-Hong Teh, Masatomo Makino, Takeshi Hoshino, Seiki Baba, Nobutaka Shimizu, Masaki Yamamoto, Takashi Kumasaka

Acta Crystallographica Section D: Biological Crystallography　71　1392-1399　2015/06/01

DOI： 10.1107/S1399004715007166 　

ISSN： 1399-0047 0907-4449
rasがん遺伝子産物の新規立体構造情報を利用した分子標的がん治療薬の開発 Invited Peer-reviewed

島扶美, 熊坂崇, 松本篤幸, 吉川陽子, 山本雅貴, 片岡徹

放射光　27　(1)　3-9　2014
湿度調節と水溶性ポリマーのコーティングを用いたタンパク質結晶マウント法 Invited Peer-reviewed

馬場清喜, 熊坂崇

日本結晶学会誌　56　194-200　2014

DOI： 10.5940/jcrsj.56.194 　
A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals Peer-reviewed

Nobuhiro Mizuno, Masatomo Makino, Takashi Kumasaka

Journal of Synchrotron Radiation　20　(6)　999-1002　2013/11

DOI： 10.1107/S0909049513021584 　

ISSN： 0909-0495 1600-5775
SPring-8 BL41XU, a high-flux macromolecular crystallography beamline Peer-reviewed

Kazuya Hasegawa, Nobutaka Shimizu, Hideo Okumura, Nobuhiro Mizuno, Seiki Baba, Kunio Hirata, Tomoyuki Takeuchi, Hiroshi Yamazaki, Yasunori Senba, Haruhiko Ohashi, Masaki Yamamoto, Takashi Kumasaka

JOURNAL OF SYNCHROTRON RADIATION　20　910-913　2013/11

DOI： 10.1107/S0909049513022176 　

ISSN： 0909-0495

eISSN： 1600-5775
Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline Peer-reviewed

Nobutaka Shimizu, Tetsuya Shimizu, Seiki Baba, Kazuya Hasegawa, Masaki Yamamoto, Takashi Kumasaka

JOURNAL OF SYNCHROTRON RADIATION　20　948-952　2013/11

DOI： 10.1107/S0909049513022887 　

ISSN： 0909-0495

eISSN： 1600-5775
Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments Peer-reviewed

Seiki Baba, Takeshi Hoshino, Len Ito, Takashi Kumasaka

Acta Crystallographica Section D: Biological Crystallography　69　(9)　1839-1849　2013/09

DOI： 10.1107/S0907444913018027 　

ISSN： 0907-4449 1399-0047
In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction Peer-reviewed

Fumi Shima, Yoko Yoshikawa, Min Ye, Mitsugu Araki, Shigeyuki Matsumoto, Jingling Liao, Lizhi Hu, Takeshi Sugimoto, Yuichi Ijiri, Azusa Takeda, Yuko Nishiyama, Chie Sato, Shin Muraoka, Atsuo Tamura, Tsutomu Osoda, Ken-ichiro Tsuda, Tomoya Miyakawa, Hiroaki Fukunishi, Jiro Shimada, Takashi Kumasaka, Masaki Yamamoto, Tohru Kataoka

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　110　(20)　8182-8187　2013/05

DOI： 10.1073/pnas.1217730110 　

ISSN： 0027-8424
Achievement of protein micro-crystallography at SPring-8 beamline BL32XU Peer-reviewed

Kunio Hirata, Yoshiaki Kawano, Go Ueno, Koichi Hashimoto, Hironori Murakami, Kazuya Hasegawa, Takaaki Hikima, Takashi Kumasaka, Masaki Yamamoto

Journal of Physics: Conference Series　425　(1)　012002-012002　2013/03
Publisher: {IOP} Publishing
DOI： 10.1088/1742-6596/425/1/012002 　

ISSN： 1742-6588
3D manipulation of protein microcrystals with optical tweezers for X-ray crystallography

T. Hikima, K. Hashimoto, H. Murakami, G. Ueno, Y. Kawano, K. Hirata, K. Hasegawa, T. Kumasaka, M. Yamamoto

Journal of Physics: Conference Series　425　(1)　2013
Publisher: Institute of Physics Publishing
DOI： 10.1088/1742-6596/425/1/012011 　

ISSN： 1742-6596 1742-6588
Development of a MEM Structure Visualization Method: Synthesis and Structural Analysis of Artificial Capsule Enclosing Protein Peer-reviewed

Mizuno Nobuhiro, Fujita Daishi, Sato Sota, Kumasaka Takashi, Fujita Makoto, Takata Masaki

J. Crystallogr. Soc. Jap　55　(3)　211-217　2013
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.55.211 　

ISSN： 0369-4585

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Proteins, sophisticated biological macromolecules, are being expected to use a wide variety of applications in the fields of industry, drug discovery and so on. However, it is now limited due to their structural instability. We first achieved to enclose the protein ubiquitin within the precisely-structured artificial capsules utilizing self-assembly process. This molecule is quite stable in various physicochemical environments. Moreover, to prove the existence of the flexible protein structure within the capsule, we developed a crystallographic method using histogram analysis of MEM electron-density（H-MED）. This method might be useful to identify flexible structures which are difficult to construct atomic models.
Dissection of Hydrogen Bond Interaction Network around an Iron-Sulfur Cluster by Site-Specific Isotope Labeling of Hyperthermophilic Archaeal Rieske-Type Ferredoxin Peer-reviewed

Toshio Iwasaki, Risako Fukazawa, Yoshiharu Miyajima-Nakano, Arngalanbaatar Baldansuren, Shinichi Matsushita, Myat T. Lin, Robert B. Gennis, Kazuya Hasegawa, Takashi Kumasaka, Sergei A. Dikanov

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY　134　(48)　19731-19738　2012/12

DOI： 10.1021/ja308049u 　

ISSN： 0002-7863
Protein encapsulation within synthetic molecular hosts Peer-reviewed

Daishi Fujita, Kosuke Suzuki, Sota Sato, Maho Yagi-Utsumi, Yoshiki Yamaguchi, Nobuhiro Mizuno, Takashi Kumasaka, Masaki Takata, Masanori Noda, Susumu Uchiyama, Koichi Kato, Makoto Fujita

NATURE COMMUNICATIONS　3　2012/10

DOI： 10.1038/ncomms2093 　

ISSN： 2041-1723
Fine-needle capillary mounting for protein microcrystals Peer-reviewed

Masatomo Makino, Izumi Wada, Nobuhiro Mizuno, Kunio Hirata, Nobutaka Shimizu, Takaaki Hikima, Masaki Yamamoto, Takashi Kumasaka

JOURNAL OF APPLIED CRYSTALLOGRAPHY　45　785-788　2012/08

DOI： 10.1107/S0021889812024545 　

ISSN： 1600-5767
Glutathione Ethylester, a Novel Protein Refolding Reagent, Enhances both the Efficiency of Refolding and Correct Disulfide Formation Peer-reviewed

Len Ito, Masaki Okumura, Kohsaku Tao, Yusuke Kasai, Shunsuke Tomita, Akiko Oosuka, Hidetoshi Yamada, Tomohisa Shibano, Kentaro Shiraki, Takashi Kumasaka, Hiroshi Yamaguchi

PROTEIN JOURNAL　31　(6)　499-503　2012/08

DOI： 10.1007/s10930-012-9427-4 　

ISSN： 1572-3887

eISSN： 1573-4943
Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants Peer-reviewed

Shin Muraoka, Fumi Shima, Mitsugu Araki, Tomoko Inoue, Akiko Yoshimoto, Yuichi Ijiri, Nobuaki Seki, Atsuo Tamura, Takashi Kumasaka, Masaki Yamamoto, Tohru Kataoka

FEBS LETTERS　586　(12)　1715-1718　2012/06

DOI： 10.1016/j.febslet.2012.04.058 　

ISSN： 0014-5793
Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel Peer-reviewed

Xu Zhang, Wenlin Ren, Paul DeCaen, Chuangye Yan, Xiao Tao, Lin Tang, Jingjing Wang, Kazuya Hasegawa, Takashi Kumasaka, Jianhua He, Jiawei Wang, David E. Clapham, Nieng Yan

NATURE　486　(7401)　130-U160　2012/06

DOI： 10.1038/nature11054 　

ISSN： 0028-0836
Upgrade of automated sample exchanger SPACE Peer-reviewed

Hironori Murakami, Go Ueno, Nobutaka Shimizu, Takashi Kumasaka, Masaki Yamamoto

JOURNAL OF APPLIED CRYSTALLOGRAPHY　45　234-238　2012/04

DOI： 10.1107/S0021889812003585 　

ISSN： 0021-8898
Crystallization and preliminary crystallographic analysis of the complex between triiodothyronine and the bb ' fragment of rat protein disulfide isomerase Peer-reviewed

Shoko Hashimoto, Len Ito, Masaki Okumura, Tomohisa Shibano, Marina Nawata, Takashi Kumasaka, Hiroshi Yamaguchi, Susumu Imaoka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　68　476-478　2012/04

DOI： 10.1107/S1744309112007439 　

ISSN： 1744-3091

eISSN： 2053-230X
Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq Peer-reviewed

Tatsuhiko Someya, Seiki Baba, Mai Fujimoto, Gota Kawai, Takashi Kumasaka, Kouji Nakamura

NUCLEIC ACIDS RESEARCH　40　(4)　1856-1867　2012/02

DOI： 10.1093/nar/gkr892 　

ISSN： 0305-1048

eISSN： 1362-4962
Structure of Thermus thermophilus homoisocitrate dehydrogenase in complex with a designed inhibitor Peer-reviewed

Eriko Nango, Takashi Yamamoto, Takashi Kumasaka, Tadashi Eguchi

JOURNAL OF BIOCHEMISTRY　150　(6)　607-614　2011/12

DOI： 10.1093/jb/mvr097 　

ISSN： 0021-924X

eISSN： 1756-2651
A rapid and robust method for selective isotope labeling of proteins Peer-reviewed

Myat T. Lin, Lindsay J. Sperling, Heather L. Frericks Schmidt, Ming Tang, Rimma I. Samoilova, Takashi Kumasaka, Toshio Iwasaki, Sergei A. Dikanov, Chad M. Rienstra, Robert B. Gennis

METHODS　55　(4)　370-378　2011/12

DOI： 10.1016/j.ymeth.2011.08.019 　

ISSN： 1046-2023

eISSN： 1095-9130
Assembly of homogeneous norovirus-like particles accomplished by amino acid substitution Peer-reviewed

Yuichi Someya, Haruko Shirato, Kazuya Hasegawa, Takashi Kumasaka, Naokazu Takeda

JOURNAL OF GENERAL VIROLOGY　92　(10)　2320-2323　2011/10

DOI： 10.1099/vir.0.033985-0 　

ISSN： 0022-1317
ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization Peer-reviewed

Toshio Iwasaki, Reinhard Kappl, Gerhard Bracic, Nobutaka Shimizu, Daijiro Ohmori, Takashi Kumasaka

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY　16　(6)　923-935　2011/08

DOI： 10.1007/s00775-011-0793-8 　

ISSN： 0949-8257
Crystal Structures and Enzymatic Properties of a Triamine/Agmatine Aminopropyltransferase from Thermus thermophilus Peer-reviewed

Mio Ohnuma, Tadashi Ganbe, Yusuke Terui, Masaru Niitsu, Takao Sato, Nobuo Tanaka, Masatada Tamakoshil, Keijiro Samejima, Takashi Kumasaka, Tairo Oshima

JOURNAL OF MOLECULAR BIOLOGY　408　(5)　971-986　2011/05

DOI： 10.1016/j.jmb.2011.03.025 　

ISSN： 0022-2836
Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring alpha-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases Peer-reviewed

Kousuke Matsumoto, Fumi Shima, Shin Muraoka, Mitsugu Araki, Lizhi Hu, Yuichi Ijiri, Rina Hirai, Jingling Liao, Takashi Yoshioka, Takashi Kumasaka, Masaki Yamamoto, Atsuo Tamura, Tohru Kataoka

JOURNAL OF BIOLOGICAL CHEMISTRY　286　(17)　15403-15412　2011/04

DOI： 10.1074/jbc.M110.204933 　

ISSN： 0021-9258
High-resolution X-ray analysis reveals binding of arginine to aromatic residues of lysozyme surface: implication of suppression of protein aggregation by arginine Peer-reviewed

Len Ito, Kentaro Shiraki, Takanori Matsuura, Masaki Okumura, Kazuya Hasegawa, Seiki Baba, Hiroshi Yamaguchi, Takashi Kumasaka

PROTEIN ENGINEERING DESIGN & SELECTION　24　(3)　269-274　2011/03

DOI： 10.1093/protein/gzq101 　

ISSN： 1741-0126
Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation Peer-reviewed

Len Ito, Kentaro Shiraki, Masatomo Makino, Kazuya Hasegawa, Takashi Kumasaka

FEBS Letters　585　(3)　555-560　2011/02/04

DOI： 10.1016/j.febslet.2011.01.008 　

ISSN： 0014-5793
Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation Peer-reviewed

Len Ito, Kentaro Shiraki, Masatomo Makino, Kazuya Hasegawa, Takashi Kumasaka

FEBS LETTERS　585　(3)　555-560　2011/02

DOI： 10.1016/j.febslet.2011.01.008 　

ISSN： 0014-5793
A Calcium-Dependent Xylan-Binding Domain of Alkaline Xylanase from Alkaliphilic Bacillus sp Strain 41M-1 Peer-reviewed

Risa Yazawa, Jun Takakura, Tomoko Sakata, Ihsanawati, Rie Yatsunami, Toshiaki Fukui, Takashi Kumasaka, Nobuo Tanaka, Satoshi Nakamura

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　75　(2)　379-381　2011/02

DOI： 10.1271/bbb.100730 　

ISSN： 0916-8451

eISSN： 1347-6947
Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii Peer-reviewed

Takeshi Hoshino, Eriko Nango, Seiki Baba, Tadashi Eguchi, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　67　(1)　101-103　2011/01

DOI： 10.1107/S1744309110046944 　

ISSN： 1744-3091
Structural Basis for Conformational Dynamics of GTP-bound Ras Protein Peer-reviewed

Fumi Shima, Yuichi Ijiri, Shin Muraoka, Jingling Liao, Min Ye, Mitsugu Araki, Kousuke Matsumoto, Naoki Yamamoto, Takeshi Sugimoto, Yoko Yoshikawa, Takashi Kumasaka, Masaki Yamamoto, Atsuo Tamura, Tohru Kataoka

JOURNAL OF BIOLOGICAL CHEMISTRY　285　(29)　22696-22705　2010/07

DOI： 10.1074/jbc.M110.125161 　

ISSN： 0021-9258
Crystallization and preliminary X-ray diffraction studies of hyperthermophilic archaeal Rieske-type ferredoxin (ARF) from Sulfolobus solfataricus P1 Peer-reviewed

Asako Kounosu, Kazuya Hasegawa, Toshio Iwasaki, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　66　842-845　2010/06

DOI： 10.1107/S1744309110019263 　

ISSN： 1744-3091

eISSN： 2053-230X
SPring-8 structural biology beamline Invited Peer-reviewed

Takashi Kumasaka, Nobutaka Shimizu, Seiki Baba, Kazuya Hasegawa, Go Ueno, Masaki Yamamoto

Yakugaku Zasshi　130　(5)　649-655　2010/05

DOI： 10.1248/yakushi.130.649 　

ISSN： 0031-6903 1347-5231
Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer Peer-reviewed

Seiki Baba, Tatsuhiko Someya, Gota Kawai, Kouji Nakamura, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　66　563-566　2010/05

DOI： 10.1107/S1744309110009942 　

ISSN： 1744-3091
Improvement in Stability of SPring-8 Standard X-Ray Monochromators with Water-Cooled Crystals

Hiroshi Yamazaki, Yasuhiro Shimizu, Takanori Miura, Masayuki Tanaka, Hikaru Kishimoto, Yasuhisa Matsuzaki, Nobtaka Shimizu, Yoshiaki Kawano, Takashi Kumasaka, Masaki Yamamoto, Tomoyuki Koganezawa, Masugu Sato, Ichiro Hirosawa, Yasunori Senba, Haruhiko Ohashi, Shunji Goto, Tetsuya Ishikawa

SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION　1234　785-+　2010

DOI： 10.1063/1.3463329 　

ISSN： 0094-243X
New micro-beam beamline at SPring-8, targeting at protein micro-crystallography Peer-reviewed

Kunio Hirata, Go Ueno, Atsushi Nisawa, Yoshiaki Kawano, Takaaki Hikima, Nobutaka Shimizu, Takashi Kumasaka, Hirokatsu Yumoto, Takashi Tanaka, Sunao Takahashi, Kunikazu Takeshita, Haruhiko Ohashi, Shunji Goto, Hideo Kitamura, Masaki Yamamoto

SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION　1234　901-+　2010

DOI： 10.1063/1.3463362 　

ISSN： 0094-243X
Present status of SPring-8 macromolecular crystallography beamlines Peer-reviewed

Yoshiaki Kawano, Nobutaka Shimizu, Seiki Baba, Kazuya Hasegawa, Masatomo Makino, Nobuhiro Mizuno, Takeshi Hoshino, Ren Ito, Izumi Wada, Kunio Hirata, Go Ueno, Takaaki Hikima, Hironori Murakami, Daisuke Maeda, Atsushi Nisawa, Takashi Kumasaka, Masaki Yamamoto

SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION　1234　359-+　2010

DOI： 10.1063/1.3463212 　

ISSN： 0094-243X
Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography Peer-reviewed

Kazuya Hasegawa, Kunio Hirata, Tetsuya Shimizu, Nobutaka Shimizu, Takaaki Hikima, Seiki Baba, Takashi Kumasaka, Masaki Yamamoto

JOURNAL OF APPLIED CRYSTALLOGRAPHY　42　(6)　1165-1175　2009/12

DOI： 10.1107/S0021889809042277 　

ISSN： 0021-8898
Crystal structure of 3-isopropylmalate dehydrogenase in complex with NAD(+) and a designed inhibitor Peer-reviewed

Eriko Nango, Takashi Yamamoto, Takashi Kumasaka, Tadashi Eguchi

BIOORGANIC & MEDICINAL CHEMISTRY　17　(22)　7789-7794　2009/11

DOI： 10.1016/j.bmc.2009.09.025 　

ISSN： 0968-0896
Crystallization and preliminary X-ray analysis of the stress-response PPM phosphatase RsbX from Bacillus subtilis Peer-reviewed

Masatoshi Suganuma, Aik Hong Teh, Masatomo Makino, Nobutaka Shimizu, Tomonori Kaneko, Kunio Hirata, Masaki Yamamoto, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　65　1128-1130　2009/11

DOI： 10.1107/S1744309109038846 　

ISSN： 1744-3091
Structural Basis of the Catalytic Mechanism Operating in Open-Closed Conformers of Lipocalin Type Prostaglandin D Synthase Peer-reviewed

Takashi Kumasaka, Kosuke Aritake, Hideo Ago, Daisuke Irikura, Toshiharu Tsurumura, Masaki Yamamoto, Masashi Miyano, Yoshihiro Urade, Osamu Hayaishi

JOURNAL OF BIOLOGICAL CHEMISTRY　284　(33)　22344-22352　2009/08

DOI： 10.1074/jbc.M109.018341 　

ISSN： 0021-9258
Expression, crystallization and preliminary crystallographic analysis of the PAS domain of RsbP, a stress-response phosphatase from Bacillus subtilis Peer-reviewed

Masatomo Makino, Shinpei Kondo, Tomonori Kaneko, Seiki Baba, Kunio Hirata, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　65　559-561　2009/06

DOI： 10.1107/S1744309109014158 　

ISSN： 1744-3091
Improvement of Alkaliphily of Bacillus Alkaline Xylanase by Introducing Amino Acid Substitutions Both on Catalytic Cleft and Protein Surface Peer-reviewed

Hirohito Umemoto, Ihsanawati, Mayuko Inami, Rie Yatsunami, Toshiaki Fukui, Takashi Kumasaka, Nobuo Tanaka, Satoshi Nakamura

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　73　(4)　965-967　2009/04

DOI： 10.1271/bbb.80869 　

ISSN： 0916-8451

eISSN： 1347-6947
[Aims and perspectives of protein micro-crystallography].

Hirata, K., Shimizu, N., Ueno, G., Kumasaka, T., Yamamoto, M.

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme　54　(12 Suppl)　2009
蛋白質微小結晶構造解析：その極限でめざすもの Invited Peer-reviewed

平田邦生, 清水伸隆, 上野剛, 熊坂崇, 山本雅貴

蛋白質核酸酵素　54　1477-1483　2009
Crystallization and preliminary X-ray diffraction studies of the prototypal homologue of mitoNEET (Tth-NEET0026) from the extreme thermophile Thermus thermophilus HB8 Peer-reviewed

Asako Kounosu, Toshio Iwasaki, Seiki Baba, Yoko Hayashi-Iwasaki, Tairo Oshima, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　64　1146-1148　2008/12

DOI： 10.1107/S1744309108035975 　

ISSN： 1744-3091

eISSN： 2053-230X
Structure of Cu/Zn superoxide dismutase from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6 Peer-reviewed

Aik-Hong Teh, Shin Kanamasa, Susumu Kajiwara, Takashi Kumasaka

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　374　(3)　475-478　2008/09

DOI： 10.1016/j.bbrc.2008.07.046 　

ISSN： 0006-291X
Crystallization and preliminary X-ray analysis of vicenisaminyltransferase VinC Peer-reviewed

Eriko Nango, Atsushi Minami, Takashi Kumasaka, Tadashi Eguchi

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　64　558-560　2008/06

DOI： 10.1107/S1744309108014681 　

ISSN： 1744-3091
Mail-in data collection at SPring-8 protein crystallography beamlines Peer-reviewed

Nobuo Okazaki, Kazuya Hasegawa, Go Ueno, Hironori Murakami, Takashi Kumasaka, Masaki Yamamoto

JOURNAL OF SYNCHROTRON RADIATION　15　(3)　288-291　2008/05

DOI： 10.1107/S0909049507064679 　

ISSN： 0909-0495
Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD(+) Peer-reviewed

Eriko Nango, Takashi Kumasaka, Toshifumi Hirayama, Nobuo Tanaka, Tadashi Eguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　70　(2)　517-527　2008/02

DOI： 10.1002/prot.21526 　

ISSN： 0887-3585
1S6-6 Two novel beamlines to achieve protein micro-crystallography(1S6 Cutting edge of protein crystallography with synchrotron radiation,The 46th Annual Meeting of the Biophysical Society of Japan)

Hirata Kunio, Nisawa Atsushi, Ueno Go, Shimizu Nobutaka, Kumasaka Takashi, Tanaka Takashi, Takahashi Sunao, Takeshita Kunikazu, Ohashi Haruhiko, Goto Shunji, Kitamura Hideo, Yamamoto Masaki, Matsugaki Naohiro, Yamada Yusuke, Hiraki Masahiko, Igarashi Noriyuki, Yamamoto Shigeru, Tsuchiya Kimichika, Shioya Tatsuro, Maezawa Hideki, Asaoka Seiji, Miyauchi Hiroshi, Tahara Toshihiro, Tanimoto Yasunori, Wakatsuki Soichi

Seibutsu Butsuri　48　(supplement)　S6　2008
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.48.s6_1 　

ISSN： 0582-4052

eISSN： 1347-4219
Preliminary studies of long wavelength X-ray diffraction experiment for protein crystallography in SAGA-LS Peer-reviewed

KAWAMOTO Masahide, SHIMIZU Nobutaka, BABA Seiki, HIRATA Kunio, ISHIJI Kotaro, SUMITANI Kazushi, MOTOSHIMA Hiroyuki, OKAJIMA Toshihiro, KUMASAKA Takashi, WATANABE Keiichi, YAMAMOTO Masaki

21　(4)　194-203　2008
Publisher:
ISSN： 0914-9287
Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004 Peer-reviewed

Toshio Iwasaki, Daijiro Ohmori, Nobutaka Shimizu, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　63　1014-1016　2007/12

DOI： 10.1107/S1744309107045757 　

ISSN： 1744-3091
Crystal structures of blasticidin S deaminase (BSD) - Implications for dynamic properties of catalytic zinc Peer-reviewed

Takashi Kumasaka, Masaki Yamamoto, Makio Furuichi, Masayoshi Nakasako, Aik-Hong Teh, Makoto Kimura, Isamu Yamaguchi, Tatzuo Ueki

JOURNAL OF BIOLOGICAL CHEMISTRY　282　(51)　37103-37111　2007/12

DOI： 10.1074/jbc.M704476200 　

ISSN： 0021-9258
Expression, purification, crystallization and preliminary X-ray analysis of the Met244Ala variant of catalase-peroxidase (KatG) from the haloarchaeon Haloarcula marismortui Peer-reviewed

Ten-i Tomomi, Takashi Kumasaka, Wataru Higuchi, Satoru Tanaka, Katsuhiko Yoshimatsu, Taketomo Fujiwara, Takao Sato

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　63　940-943　2007/11

DOI： 10.1107/S1744309107046489 　

ISSN： 1744-3091
The 1.3 angstrom crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 Peer-reviewed

Guntur Fibriansah, Sumiko Masuda, Naoya Koizumi, Satoshi Nakamura, Takashi Kumasaka

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　69　(3)　683-690　2007/11

DOI： 10.1002/prot.21589 　

ISSN： 0887-3585
Cloning and functional characterization of the copper/zinc superoxide dismutase gene from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6 Peer-reviewed

Shin Kanamasa, Koichiro Sumi, Naho Yamuki, Takashi Kumasaka, Takeshi Miura, Fumiyoshi Abe, Susumu Kajiwara

MOLECULAR GENETICS AND GENOMICS　277　(4)　403-412　2007/04

DOI： 10.1007/s00438-006-0197-6 　

ISSN： 1617-4615
Characterization of Nocardiopsis beta-1,3-glucanase with additional carbohydrate-binding domains. International-journal

Naoya Koizumi, Yuya Isoda, Kiyoe Maeda, Sumiko Masuda, Gunter Fibriansah, Takashi Kumasaka, Rie Yatsunami, Toshiaki Fukui, Satoshi Nakamura

Nucleic acids symposium series (2004)　(51)　459-60　2007

eISSN： 1746-8272

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beta-1,3-Glucanase F (BglF) from alkaliphilic Nocardiopsis sp. F96 is a single domain enzyme composed of only a catalytic domain. Chimeric BglFs with some carbohydrate-binding domains were constructed and characterized. By connecting the C-terminal additional domain of beta-1,3-glucanase H from Bacillus circulans IAM1165 and the chitin-binding domain of chitinase J from alkaliphilic Bacillus sp. J813, binding ability and hydrolyzing activity toward insoluble beta-1,3-glucans were both improved.
Contribution of salt bridges to alkaliphily of Bacillus alkaline xylanase. International-journal

Hirohito Umemoto, Ihsanawati, Mayuko Inami, Rie Yatsunami, Toshiaki Fukui, Takashi Kumasaka, Nobuo Tanaka, Satoshi Nakamura

Nucleic acids symposium series (2004)　(51)　461-2　2007

eISSN： 1746-8272

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Xylanase J (XynJ) from alkaliphilic Bacillussp. strain 41M-1 is an alkaline xylanase. Structure comparison indicated that there were several specific salt bridges in the catalytic cleft of XynJ compared with neutral xylanases. Mutant enzymes were prepared by substituting several amino acids comprising the salt bridges. Some mutants exhibited acidophilic shift in optimum pH, whereas another showed alkaliphilic shift. These results suggested that the characteristic salt bridges could contribute to the alkaliphily of XynJ.
1P067 The micro-focus beamline to open the new field of protein micro-crystallography(Proteins-functions, methodology, and protein enigineering,Oral Presentations)

Hirata Kunio, Nisawa Atsushi, Ueno Go, Shimizu Nobutaka, Kumasaka Takashi, Yamamoto Masaki

Seibutsu Butsuri　47　S40　2007
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.47.S40_2 　
Resonance Raman characterization of archaeal and bacterial Rieske protein variants with modified hydrogen bond network around the [2Fe-2S] center Peer-reviewed

Toshio Iwasaki, Asako Kounosu, Derrick R. J. Kolling, Sangmoon Lhee, Antony R. Crofts, Sergei A. Dikanov, Takuro Uchiyama, Takashi Kumasaka, Hiroyuki Ishikawa, Miwa Kono, Takeo Imai, Akio Urushiyama

PROTEIN SCIENCE　15　(8)　2019-2024　2006/08

DOI： 10.1110/ps.052035406 　

ISSN： 0961-8368
The 1.48 angstrom resolution crystal structure of the homotetrameric cytidine deaminase from mouse Peer-reviewed

AH Teh, M Kimura, M Yamamoto, N Tanaka, Yamaguchi, I, T Kumasaka

BIOCHEMISTRY　45　(25)　7825-7833　2006/06

DOI： 10.1021/bi060345f 　

ISSN： 0006-2960
Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes Peer-reviewed

T Matsui, K Hogetsu, J Usukura, T Sato, T Kumasaka, Y Akao, N Tanaka

GENES TO CELLS　11　(4)　439-452　2006/04

DOI： 10.1111/j.1365-2443.2006.00951.x 　

ISSN： 1356-9597
RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation Peer-reviewed

Go Ueno, Hiroyuki Kanda, Raita Hirose, Koh Ida, Takashi Kumasaka, Masaki Yamamoto

Journal of Structural and Functional Genomics　7　(1)　15-22　2006/03

DOI： 10.1007/s10969-005-9005-5 　

ISSN： 1345-711X
Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp strain F96 Peer-reviewed

G Fibriansah, S Masuda, R Hirose, K Hamada, N Tanaka, S Nakamura, T Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　62　20-22　2006/01

DOI： 10.1107/S174430910503900X 　

ISSN： 1744-3091
Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site Peer-reviewed

Iwasaki, T., Ohmori, D., Kounosu, A., Kumasaka, T.

Acta Crystallographica Section F: Structural Biology and Crystallization Communications　62　(10)　993-995　2006

DOI： 10.1107/S1744309106034476 　
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8 Peer-reviewed

Ihsanawati, T Kumasaka, T Kaneko, C Morokuma, R Yatsunami, T Sato, S Nakamura, N Tanaka

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　61　(4)　999-1009　2005/12

DOI： 10.1002/prot.20700 　

ISSN： 0887-3585
A norovirus protease structure provides insights into active and substrate binding site integrity Peer-reviewed

K Nakamura, Y Someya, T Kumasaka, G Ueno, M Yamamoto, T Sato, N Takeda, T Miyamura, N Tanaka

JOURNAL OF VIROLOGY　79　(21)　13685-13693　2005/11

DOI： 10.1128/JVI.79.21.13685-13693.2005 　

ISSN： 0022-538X
Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics Peer-reviewed

E Nango, T Kumasaka, T Sato, N Tanaka, KA Katsumi, T Eguchi

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　61　709-711　2005/07

DOI： 10.1107/S1744309105018841 　

ISSN： 1744-3091
Beamline Scheduling Software: administration software for automatic operation of the RIKEN structural genomics beamlines at SPring-8 Peer-reviewed

G Ueno, H Kanda, T Kumasaka, M Yamamoto

JOURNAL OF SYNCHROTRON RADIATION　12　380-384　2005/05

DOI： 10.1107/S0909049505004735 　

ISSN： 0909-0495
Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis Peer-reviewed

T Kaneko, N Tanaka, T Kumasaka

PROTEIN SCIENCE　14　(2)　558-565　2005/02

DOI： 10.1110/ps.041170005 　

ISSN： 0961-8368
Crystallization and preliminary X-ray studies on the reaction center-light-harvesting 1 core complex from Rhodopseudomonas viridis Peer-reviewed

S Saijo, T Sato, T Kumasaka, N Tanaka, K Harata, T Odahara

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　61　83-86　2005/01

DOI： 10.1107/S1744309104028945 　

ISSN： 1744-3091
Sample management system for a vast amount of frozen crystals at SPring-8 Peer-reviewed

G Ueno, R Hirose, K Ida, T Kumasaka, M Yamamoto

JOURNAL OF APPLIED CRYSTALLOGRAPHY　37　867-873　2004/12

DOI： 10.1107/S0021889804019296 　

ISSN： 1600-5767
Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiFl) from the alkaliphilic Nocardiopsis sp strain F96 Peer-reviewed

T Matsui, T Kumasaka, K Endo, T Sato, S Nakamura, N Tanaka

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　60　2016-2018　2004/11

DOI： 10.1107/S0907444904020475 　

ISSN： 0907-4449
Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment Peer-reviewed

T Uchiyama, A Kounosu, T Sato, N Tanaka, T Iwasaki, T Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　60　1487-1489　2004/08

DOI： 10.1107/S0907444904014295 　

ISSN： 0907-4449
Structural Basis of leukotriene B-4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase Catalytic Mechanism and a Possible SH3-binding Loop Peer-reviewed

T Hori, T Yokomizo, H Ago, M Sugahara, G Ueno, M Yamamoto, T Kumasaka, T Shimizu, M Miyano

FASEB JOURNAL　18　(8)　C281-C281　2004/05

ISSN： 0892-6638
Structural basis of leukotriene B-4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop Peer-reviewed

T Hori, T Yokomizo, H Ago, M Sugahara, G Ueno, M Yamamoto, T Kumasaka, T Shimizu, M Miyano

JOURNAL OF BIOLOGICAL CHEMISTRY　279　(21)　22615-22623　2004/05

DOI： 10.1074/jbc.M312655200 　

ISSN： 0021-9258
Erratum: Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain (Journal of Biological Chemistry (2003) 278 (48162-48168))

Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., Tanaka, N.

Journal of Biological Chemistry　279　(6)　2004
High throughput protein crystallography at RIKEN structural genomic beamlines Peer-reviewed

G Ueno, M Yamamoto, R Hirose, K Ida, H Kanda, M Miyano, T Kumasaka, T Ishikawa

SYNCHROTRON RADIATION INSTRUMENTATION　705　1209-1212　2004

ISSN： 0094-243X
Crystallization and X-ray analysis of the N-terminal core domain of a tumour-associated human DEAD-box RNA helicase, rck/p54 Peer-reviewed

T Matsui, K Hogetsu, Y Akao, M Tanaka, T Sato, T Kumasaka, N Tanaka

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　60　156-159　2004/01

DOI： 10.1107/S0907444903024223 　

ISSN： 0907-4449
Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain Peer-reviewed

T Kaneko, T Kumasaka, T Ganbe, T Sato, K Miyazawa, N Kitamura, N Tanaka

JOURNAL OF BIOLOGICAL CHEMISTRY　278　(48)　48162-48168　2003/11

DOI： 10.1074/jbc.M306677200 　

ISSN： 0021-9258
Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima Peer-reviewed

Ihsanawati, T Kumasaka, T Kaneko, C Morokuma, S Nakamura, N Tanaka

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　59　1659-1661　2003/09

DOI： 10.1107/S0907444903015397 　

ISSN： 0907-4449
Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor Peer-reviewed

H Imamura, S Fushinobu, M Yamamoto, T Kumasaka, BS Jeon, T Wakagi, H Matsuzawa

JOURNAL OF BIOLOGICAL CHEMISTRY　278　(21)　19378-19386　2003/05

DOI： 10.1074/jbc.M213134200 　

ISSN： 0021-9258
Mechanism of metal activation of human hematopoietic prostaglandin D synthase Peer-reviewed

T Inoue, D Irikura, N Okazaki, S Kinugasa, H Matsumura, N Uodome, M Yamamoto, T Kumasaka, M Miyano, Y Kai, Y Urade

NATURE STRUCTURAL BIOLOGY　10　(4)　291-296　2003/04

DOI： 10.1038/nsb907 　

ISSN： 1072-8368
Development of Structure Analysis by MAD Method Invited Peer-reviewed

KUMASAKA Takashi, YAMAMOTO Masaki

X-RAYS　45　(1)　14-18　2003
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.45.14 　

ISSN： 0369-4585

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The crystallographic phase problem had not been routinely solved in protein crystallography. Nowadays, MAD method is widely used for crystallographic determination of unknown protein structures, since the scope of MAD application has been extended by the use of synchrotron radiation facilities, protein expression techniques, and computational development. The method has paved the way to high-throughput structure determination of protein crystals and introduced to structural genomics study. We describe here a brief summary of MAD method and its experimental.
Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme Peer-reviewed

D Irikura, T Kumasaka, M Yamamoto, H Ago, M Miyano, KB Kubata, H Sakai, O Hayaishi, Y Urade

JOURNAL OF BIOCHEMISTRY　133　(1)　29-32　2003/01

DOI： 10.1093/jb/mvg006 　

ISSN： 0021-924X
Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography Peer-reviewed

T Kumasaka, M Yamamoto, E Yamashita, H Moriyama, T Ueki

STRUCTURE　10　(9)　1205-1210　2002/09

DOI： 10.1016/S0969-2126(02)00830-4 　

ISSN： 0969-2126
Crystal structure of lipocalin-type prostaglandin D synthase Peer-reviewed

D Irikura, T Kumasaka, M Yamamoto, O Hayaishi, Y Urade

OXYGEN AND LIFE: OXYGENASES, OXIDASE AND LIPID MEDIATORS　1233　453-459　2002

ISSN： 0531-5131
ロドプシンの構造決定がひらくゲノム創薬の新しい道 Invited Peer-reviewed

堀哲哉, 熊坂崇, 山本雅貴, 宮野雅司

バイオベンチャー　2　73-79　2002
The flexible C-terminal region of Aspergillus terreus blasticidin S deaminase: Identification of its functional roles with deletion enzymes Peer-reviewed

M Kimura, M Furuichi, M Yamamoto, T Kumasaka, H Mizuno, M Miyano, Yamaguchi, I

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　290　(1)　421-426　2002/01

DOI： 10.1006/bbrc.2001.6184 　

ISSN： 0006-291X
Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter Peer-reviewed

TH Tahirov, K Sato, E Ichikawa-Iwata, M Sasaki, T Inoue-Bungo, M Shiina, K Kimura, S Takata, A Fujikawa, H Morii, T Kumasaka, M Yamamoto, S Ishii, K Ogata

CELL　108　(1)　57-70　2002/01

DOI： 10.1016/S0092-8674(01)00636-5 　

ISSN： 0092-8674
Crystals of ternary protein-DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBP alpha or C/EBP beta and tom-1A promoter fragment Peer-reviewed

TH Tahirov, M Sasaki, T Inoue-Bungo, A Fujikawa, K Sato, T Kumasaka, M Yamamoto, K Ogata

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　57　1655-1658　2001/11

DOI： 10.1107/S0907444901011982 　

ISSN： 0907-4449
The 1.55 angstrom resolution structure of Nicotiana alata S-F11-RNase associated with gametophytic self-incompatibility Peer-reviewed

K Ida, S Norioka, M Yamamoto, T Kumasaka, E Yamashita, E Newbigin, AE Clarke, F Sakiyama, M Sato

JOURNAL OF MOLECULAR BIOLOGY　314　(1)　103-112　2001/11

DOI： 10.1006/jmbi.2001.5127 　

ISSN： 0022-2836
Development of high-speed Imaging Plate detector Peer-reviewed

M Yamamoto, T Kumasaka, H Yamazaki, K Sasaki, Y Yokozawa, T Ishikawa

NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT　467　1160-1162　2001/07

DOI： 10.1016/S0168-9002(01)00583-6 　

ISSN： 0168-9002
Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein-DNA complexes with involvement of AML1/Runx-1/CBF alpha Runt domain, CBF beta and the C/EBP beta bZip region Peer-reviewed

TH Tahirov, T Inoue-Bungo, M Sasaki, M Shiina, K Kimura, K Sato, T Kumasaka, M Yamamoto, N Kamiya, K Ogata

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　57　850-853　2001/06

DOI： 10.1107/S0907444901003900 　

ISSN： 0907-4449
[Atomic structure of bovine rhodopsin, a seven transmembrane receptor: toward the elucidation of GPCR's molecular mechanism]

Miyano M, Kumasaka T, Hori T, Yamamoto M

2001/05
Erratum: Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFβ (Cell 104:5(755-767))

Tahirov, T.H., Inoue-Bungo, T., Morii, H., Fujikawa, A., Sasaki, M., Kimura, K., Shiina, M., Sato, K., Kumasaka, T., Yamamoto, M., Ishhi, S., Ogata, K.

Cell　105　(2)　291　2001/04/20

DOI： 10.1016/S0092-8674(01)00319-1 　

ISSN： 0092-8674
Crystal Structure of rhodopsin: a G-protein coupled receptor Peer-reviewed

K Palczewski, T Okada, RE Stenkamp, DCDC Teller, CA Behnke, T Kumasaka, T Hori, H Motoshima, M Yamamoto, M Miyano

FASEB JOURNAL　15　(4)　A29-A29　2001/03

ISSN： 0892-6638
Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms Peer-reviewed

T Hori, T Kumasaka, M Yamamoto, T Nonaka, N Tanaka, Y Hashimoto, T Ueki, K Takio

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　57　361-368　2001/03

DOI： 10.1107/S0907444900019740 　

ISSN： 0907-4449
Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBF beta Peer-reviewed

TH Tahirov, T Inoue-Bungo, H Morii, A Fujikawa, M Sasaki, K Kimura, M Shiina, K Sato, T Kumasaka, M Yamamoto, S Ishii, K Ogata

CELL　104　(5)　755-767　2001/03

DOI： 10.1016/S0092-8674(01)00271-9 　

ISSN： 0092-8674
Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling Peer-reviewed

FA Samatey, K Imada, S Nagashima, F Vonderviszt, T Kumasaka, M Yamamoto, K Namba

NATURE　410　(6826)　331-337　2001/03

DOI： 10.1038/35066504 　

ISSN： 0028-0836
Atomic structure of bovine rhodopsin, a seven transmembrane receptor: toward the elucidation of GPCR's molecular mechanism

Miyano, M., Kumasaka, T., Hori, T., Yamamoto, M.

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme　46　(6)　2001
Crystal structure of rhodopsin: A G-protein-coupled receptor Peer-reviewed

K Palczewski, T Kumasaka, T Hori, CA Behnke, H Motoshima, BA Fox, IL Trong, DC Teller, T Okada, RE Stenkamp, M Yamamoto, M Miyano

BIOPHYSICAL JOURNAL　80　(1)　349A-349A　2001/01

ISSN： 0006-3495
Trichromatic Concept for Rapid Protein Crystallographic Analysis Invited Peer-reviewed

YAMAMOTO Masaki, KUMASAKA Takashi

Seibutsu Butsuri　41　(3)　156-159　2001
Publisher: The Biophysical Society of Japan General Incorporated Association
DOI： 10.2142/biophys.41.156 　

ISSN： 0582-4052 1347-4219
７回膜貫通型レセプター・ロドプシンの結晶構造 Invited Peer-reviewed

宮野雅司, 熊坂崇, 堀哲哉, 山本雅貴

蛋白質核酸酵素　46　(6)　687-697　2001
Publisher: 共立出版
ISSN： 0039-9450
Prospects for X-ray crystal structure analysis of selenoproteins with SPring-8 synchrotron radiation Peer-reviewed

M Yamamoto, T Kumasaka, E Yamashita, H Moriyama, M Sato, T Ueki

JOURNAL OF HEALTH SCIENCE　46　(6)　426-429　2000/12

DOI： 10.1248/jhs.46.426 　

ISSN： 1344-9702

eISSN： 1347-5207
Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch Peer-reviewed

T Toyoda, OF Tin, K Ito, T Fujiwara, T Kumasaka, M Yamamoto, MB Garber, Y Nakamura

RNA-A PUBLICATION OF THE RNA SOCIETY　6　(10)　1432-1444　2000/10

DOI： 10.1017/S1355838200001060 　

ISSN： 1355-8382
Structural basis of glutamate recognition by a dimeric metabotropic glutamate receptor Peer-reviewed

N Kunishima, Y Shimada, Y Tsuji, T Sato, M Yamamoto, T Kumasaka, S Nakanishi, H Jingami, K Morikawa

NATURE　407　(6807)　971-977　2000/10

DOI： 10.1038/35039564 　

ISSN： 0028-0836
Crystal structure of the pyridoxal 5 '-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida Peer-reviewed

H Motoshima, K Inagaki, T Kumasaka, M Furuichi, H Inoue, T Tamura, N Esaki, K Soda, N Tanaka, M Yamamoto, H Tanaka

JOURNAL OF BIOCHEMISTRY　128　(3)　349-354　2000/09

ISSN： 0021-924X
The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport Peer-reviewed

SJ Lee, N Imamotos, H Sakai, A Nakagawa, S Kose, M Koike, M Yamamoto, T Kumasaka, Y Yoneda, T Tsukihara

JOURNAL OF MOLECULAR BIOLOGY　302　(1)　251-264　2000/09

DOI： 10.1006/jmbi.2000.4055 　

ISSN： 0022-2836
Crystal structure of rhodopsin: A G protein-coupled receptor Peer-reviewed

K Palczewski, T Kumasaka, T Hori, CA Behnke, H Motoshima, BA Fox, Le Trong, I, DC Teller, T Okada, RE Stenkamp, M Yamamoto, M Miyano

SCIENCE　289　(5480)　739-745　2000/08

DOI： 10.1126/science.289.5480.739 　

ISSN： 0036-8075
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8 Peer-reviewed

M Sugahara, T Mikawa, T Kumasaka, M Yamamoto, R Kato, K Fukuyama, Y Inoue, S Kuramitsu

EMBO JOURNAL　19　(15)　3857-3869　2000/08

DOI： 10.1093/emboj/19.15.3857 　

ISSN： 0261-4189
Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases Peer-reviewed

T Nakai, T Hasegawa, E Yamashita, M Yamamoto, T Kumasaka, T Ueki, H Nanba, Y Ikenaka, S Takahashi, M Sato, T Tsukihara

STRUCTURE WITH FOLDING & DESIGN　8　(7)　729-737　2000/07

DOI： 10.1016/S0969-2126(00)00160-X 　

ISSN： 0969-2126
Small-angle X-ray scattering station at the SPring-8 RIKEN beamline Peer-reviewed

T Fujisawa, K Inoue, T Oka, H Iwamoto, T Uruga, T Kumasaka, Y Inoko, N Yagi, M Yamamoto, T Ueki

JOURNAL OF APPLIED CRYSTALLOGRAPHY　33　(1)　797-800　2000/06

DOI： 10.1107/S002188980000131X 　

ISSN： 0021-8898
X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO2 hydration Peer-reviewed

S Mitsuhashi, T Mizushima, E Yamashita, M Yamamoto, T Kumasaka, H Moriyama, T Ueki, S Miyachi, T Tsukihara

JOURNAL OF BIOLOGICAL CHEMISTRY　275　(8)　5521-5526　2000/02

DOI： 10.1074/jbc.275.8.5521 　

ISSN： 0021-9258
Introduction to Software for Protein Crystallography Invited Peer-reviewed

KUMASAKA Takashi

X-RAYS　42　(6)　474-477　2000
Publisher: The Crystallographic Society of Japan
DOI： 10.5940/jcrsj.42.474 　

ISSN： 0369-4585 1884-5576

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Crystal structure determination of proteins is not so straight forward, since the direct method for small molecules would not be applied to them. To extract the phase information from experimental measurement, methodological and technical developments have been proposed and examined. The qualification of crystals is also extended by the recent development of related techniques such as molecular biology, computation and synchrotron radiation. We summarize here the recent trend of computer software for protein crystallography.
ダイヤモンド分光器 Invited Peer-reviewed

山本雅貴, 熊坂崇, 石川哲也

ニューダイヤモンド　58　16-20　2000
Synthetic diamond monochromator at SPring-8 Invited Peer-reviewed

M. Yamamoto, T. Kumasaka, T. Ishikawa

Review of High Pressure Science and Technology/Koatsuryoku No Kagaku To Gijutsu　10　(1)　56-61　2000
Publisher: Japan Society of High Pressure Science and Technology
DOI： 10.4131/jshpreview.10.56 　

ISSN： 0917-639X
Crystallization and preliminary X-ray crystallographic studies of Thermus thermophilus HB8 MutM protein involved in repairs of oxidative DNA damage Peer-reviewed

M Sugahara, T Mikawa, R Kato, K Fukuyama, T Kumasaka, M Yamamoto, Y Inoue, S Kuramitsu

JOURNAL OF BIOCHEMISTRY　127　(1)　9-11　2000/01

DOI： 10.1093/oxfordjournals.jbchem.a022588 　

ISSN： 0021-924X

eISSN： 1756-2651
A multiple CCD X-ray detector and its first operation with synchrotron radiation X-ray beam Peer-reviewed

M Suzuki, M Yamamoto, T Kumasaka, K Sato, H Toyokawa, IF Aries, PA Jerram, T Ueki

NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT　436　(1-2)　174-181　1999/10

DOI： 10.1016/S0168-9002(99)00617-8 　

ISSN： 0168-9002
Performance of multiple-CCD X-ray detector system at SPring-8 for protein crystallography Peer-reviewed

M Suzuki, M Yamamoto, T Kumasaka, K Sato, H Toyokawa, T Ueki

DETECTORS FOR CRYSTALLOGRAPHY AND DIFFRACTION STUDIES AT SYNCHROTRON SOURCES　3774　38-45　1999

DOI： 10.1117/12.367121 　

ISSN： 0277-786X
A multiple-CCD X-ray detector and its basic characterization Peer-reviewed

M Suzuki, M Yamamoto, T Kumasaka, K Sato, H Toyokawa, IF Aries, PA Jerram, D Gullick, T Ueki

JOURNAL OF SYNCHROTRON RADIATION　6　6-18　1999/01

DOI： 10.1107/S0909049598014241 　

ISSN： 0909-0495
Evaluation of high spatial resolution imaging plate Peer-reviewed

M Yamamoto, T Kumasaka, T Uruga, N Kamiya, H Iwasaki, T Ueki

NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT　416　(2-3)　314-318　1998/10

DOI： 10.1016/S0168-9002(98)00566-X 　

ISSN： 0168-9002
Trichromatic concept at SPring-8 RIKEN beamline I Peer-reviewed

M Yamamoto, T Kumasaka, T Fujisawa, T Ueki

JOURNAL OF SYNCHROTRON RADIATION　5　222-225　1998/05

DOI： 10.1107/S0909049597014738 　

ISSN： 0909-0495
STUDIES ON THE MAD METHOD AT THE RIKEN BEAMLINE I BL45XU Invited Peer-reviewed

Yamamoto, M, Kumasaka, T, Yamashita, E

SPring-8 Research Frontiers　1997-1998　6-8　1998
３波長結晶構造解析ビームライン Invited Peer-reviewed

山本雅貴, 熊坂崇, 植木龍夫

放射光　11　107-113　1998
Crystal structure of H-2-proteinase from the venom of Trimeresurus flavoviridis Peer-reviewed

T Kumasaka, M Yamamoto, H Moriyama, N Tanaka, M Sato, Y Katsube, Y Yamakawa, T OmoriSatoh, S Iwanaga, T Ueki

JOURNAL OF BIOCHEMISTRY　119　(1)　49-57　1996/01

ISSN： 0021-924X
CRYSTALLIZATION AND PRELIMINARY-X-RAY STUDY OF H-2-PROTEINASE FROM THE VENOM OF TRIMERESURUS-FLAVOVIRIDIS Peer-reviewed

T KUMASAKA, H TAKEYA, M YAMAMOTO, Y YAMAKAWA, T OMORISATOH, H MORIYAMA, N TANAKA, M SATO, Y KATSUBE, S IWANAGA

JOURNAL OF BIOCHEMISTRY　117　(5)　929-930　1995/05

ISSN： 0021-924X

Show all ︎Show first 5

Misc. 60

SPring-8BL41XUにおける時分割構造解析環境の構築

矢野直峰, 奥村英夫, 馬場清喜, 河村高志, 村上博則, 増永拓也, BOKHOVE Marcel, LUO Fangjia, NUEMKET Nipawan, KANG Jungmin, 保坂俊彰, 長谷川和也, 長谷川和也, 山本雅貴, 南後恵理子, 南後恵理子, 熊坂崇, 熊坂崇

日本蛋白質科学会年会(Web)　25th　2025
X線結晶構造解析によるヒトF1-ATPaseの回転力発生機構の分析

鈴木俊治, 鈴木俊治, 鈴木俊治, 山下栄樹, 馬場清喜, 長谷川和也, 熊坂崇, 平田邦生, 吉田賢右, 久堀徹

日本生化学会大会(Web)　97th　2024
室温構造解析・時分割構造解析に向けたSPring-8構造生物学ビームラインの高度化

馬場清喜, 奥村英夫, 河村高志, 村上博則, 増永拓也, 長谷川和也, 山本雅貴, 熊坂崇

日本蛋白質科学会年会(Web)　23rd (CD-ROM)　2023
SPring-8生体高分子結晶解析ビームラインと創薬スクリーニングパイプラインの現状

坂井直樹, 仲村勇樹, 水野伸宏, 馬場清喜, 村上博則, 増永拓也, 奥村英夫, 河村高志, 上野剛, 平田邦生, 長谷川和也, 山本雅貴, 熊坂崇

日本蛋白質科学会年会(Web)　23rd (CD-ROM)　2023
SPring-8PX-BL結晶化プレートin situ自動回折測定技術の開発

水野伸宏, 奥村英夫, 馬場清喜, 村上博則, 増永拓也, 仲村勇樹, 坂井直樹, 河村高志, 小倉章衣, 長谷川和也, 上野剛, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2023　2023
SPring-8自動測定システムZOOの歩んだ8年間

平田邦生, 河野能顕, 上野剛, 松浦滉明, 坂井直樹, 坂井直樹, 馬場清喜, 水野伸宏, 仲村勇樹, 村上博則, 長谷川和也, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2023　2023
室温構造解析・時分割構造解析に向けたSPring-8構造生物学ビームラインの高度化

矢野直峰, 馬場清喜, 奥村英夫, 河村高志, 村上博則, 増永拓也, NIPAWAN Nuemket, NIPAWAN Nuemket, KANG Jungmin, 保坂俊彰, 長谷川和也, 山本雅貴, 南後恵理子, 熊坂崇

日本結晶学会年会講演要旨集　2023　2023
理研構造ゲノムビームラインIIの現状

上野剛, 小西真晶, 吾郷日出夫, 奥村英夫, 河村高志, 坂井直樹, 竹下浩平, 引間孝明, 平田邦生, 河野能顕, 松浦滉明, 仲村勇樹, 村上博則, 増永拓也, 馬場清喜, 水野伸宏, 長谷川和也, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
動的構造解析に向けたSPring-8BL41XUの高度化構想

長谷川和也, 馬場清喜, 河村高志, 村上博則, 増永拓也, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
共用タンパク質結晶回折ビームラインBL45XUにおける自動測定の現状

馬場清喜, 水野伸宏, 仲村勇樹, 長谷川和也, 奥村英夫, 河村高志, 村上博則, 増永拓也, 坂井直樹, 坂井直樹, 松浦滉明, 平田邦生, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
SPring-8PX-BLにおける結晶化プレートin situ回折測定を利用した化合物スクリーニングシステムの開発

奥村英夫, 坂井直樹, 坂井直樹, 村上博則, 水野伸宏, 増永拓也, 仲村勇樹, 上野剛, 馬場清喜, 河村高志, 長谷川和也, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
SPring-8タンパク質結晶回折ビームライン新遠隔測定システム

水野伸宏, 増永拓也, 長谷川和也, 上野剛, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
放射光を用いたSPring-8創薬スクリーニングパイプラインの開発

坂井直樹, 坂井直樹, 松浦滉明, 平田邦生, 竹下浩平, 奥村英夫, 水野伸宏, 村上博則, 増永拓也, 仲村勇樹, 上野剛, 馬場清喜, 長谷川和也, 熊坂崇, 山本雅貴

日本蛋白質科学会年会(Web)　22nd　2022
SPring-8BL41XUにおける常温回折測定環境の開発

奥村英夫, 馬場清喜, 長谷川和也, 河村高志, 村上博則, 増永拓也, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2022　2022
Room Temperature Serial Synchrotron Crystallography

長谷川和也, 熊坂崇

日本結晶学会誌　64　(4)　2022

ISSN： 0369-4585
SPring-8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

櫻井啓介, 山下栄樹, 吉村政人, 長谷川和也, 村上博則, 熊坂崇, 古川行人, 上野剛, 山本雅貴, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム(Web)　35th　2022
DNAミスマッチ修復系エンドヌクレアーゼであるMutLのATP結合部位におけるリンチ症候群関連の変異はMutLの構造を不安定化させる—A Lynch syndrome-associated mutation at a Bergerat ATP-binding fold destabilizes the structure of the DNA mismatch repair endonuclease MutL

出原啓介, 福井健二, 村川武志, 馬場清喜, 熊坂崇, 内山和久, 矢野貴人

大阪医科薬科大学医学会雑誌 = Journal of the Medical Association of Osaka Medical and Pharmaceutical University　80　(1・2)　85-91　2021/09
Publisher: 大阪医科薬科大学医学会 = Medical Association of Osaka Medical and Pharmaceutical University
ISSN： 2436-5939
SPring-8PX-BLにおける結晶化プレートin situ回折測定と化合物スクリーニングシステムの開発

奥村英夫, 坂井直樹, 坂井直樹, 村上博則, 水野伸宏, 増永拓也, 仲村勇樹, 上野剛, 馬場清喜, 河村高志, 長谷川和也, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2021　2021
SPring-8BL45XUで実現する高効率・高精度自動測定

馬場清喜, 水野伸宏, 仲村勇樹, 長谷川和也, 奥村英夫, 河村高志, 村上博則, 増永拓也, 坂井直樹, 坂井直樹, 松浦滉明, 平田邦生, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2021　2021
時分割構造解析に向けたSPring-8BL41UXの高度化構想

長谷川和也, 馬場清喜, 河村高志, 村上博則, 増永拓也, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2021　2021
タンパク質結晶の動力学的回折効果の観測

鈴木凌, 小泉晴比古, 平野馨一, 熊坂崇, 小島謙一, 橘勝

KEK Progress Report (Web)　(2018-7)　ROMBUNNO.206 (WEB ONLY)　2018/12

ISSN： 1344-6320
タンパク質結晶におけるX線の動力学的回折効果の観測

鈴木凌, 小泉晴比古, 小泉晴比古, 平野馨一, 熊坂崇, 小島謙一, 橘勝

Photon Factory News　36　(3)　8‐12　2018/11

ISSN： 0916-0604
データ収集・処理の自動化による多数の微小結晶を用いた構造解析の効率化

山下恵太郎, 山下恵太郎, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

KEK Proceedings (Web)　(2016-4)　161‐163 (WEB ONLY)　2017/03
フタロシアニン誘導体とテトラフェニルポルフィリンによって構成される自己組織化超分子の結晶構造:太陽電池用増感色素としての活用に向けた考察

牧野正知, 松林和彦, 兒玉由貴子, 今若直人, 水野伸宏, 熊坂崇

島根県産業技術センター研究報告　(52)　10‐16-16　2016/02
Publisher: 島根県産業技術センター
ISSN： 1345-7675
高精度迅速測定を目指したSPring-8 BL41XUの高度化

長谷川和也, 奥村英夫, 馬場清喜, 水野伸宏, 平田邦生, 山下恵太郎, 村上博則, 上野剛, 古川行人, 仙波泰徳, 湯本博勝, 小山貴久, 竹内智之, 山崎裕史, 大橋治彦, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　28th　2015
Application of 2D pulsed EPR (HYSCORE) in the structural analysis of hydrogen bond network around a biological iron-sulfur cluster

T. Iwasaki, Y. Miyajima-Nakano, R. Fukazawa, E. Hagiuda, K. Hasegawa, T. Kumasaka, A. Baldansuren, S. A. Dikanov

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY　19　S320-S320　2014/03

ISSN： 0949-8257

eISSN： 1432-1327
SPring-8構造生物学IビームラインBL41XUの高度化

長谷川和也, 奥村英夫, 平田邦生, 仙波泰徳, 湯本博勝, 竹内智之, 山崎裕史, 大橋治彦, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　27th　2014
高精度迅速測定を目指したSPring-8BL41XUの高度化

長谷川和也, 奥村英夫, 馬場清喜, 水野伸宏, 平田邦生, 山下恵太郎, 村上博則, 上野剛, 古川行人, 仙波泰徳, 湯本博勝, 小山貴久, 竹内智之, 山崎裕史, 大橋治彦, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2014　2014
高精度迅速測定に向けたSPring-8 BL41XUの高度化

長谷川和也, 長谷川和也, 奥村英夫, 平田邦生, 仙波泰徳, 湯本博勝, 竹内智之, 山崎裕史, 大橋治彦, 山本雅貴, 熊坂崇, 熊坂崇

日本結晶学会年会講演要旨集　2013　2013
アミロイド前駆体タンパク質の可溶性細胞外領域sAPPαのpH依存的構造変化

金村進吾, 奥村正樹, 油谷克英, 浜田大三, 引間孝明, 伊藤廉, 伊藤廉, 前川拓摩, 熊坂崇, 新延道夫, 山口宏, 日高雄二

日本蛋白質科学会年会プログラム・要旨集　12th　2012
抗凍結剤を低減できるタンパク質結晶のマウント方法

馬場清喜, 星野武司, 伊藤廉, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　25th　2012
ターゲットタンパクプログラムに向けた放射光ビームライン開発

山本雅貴, 平田邦生, 河野能顕, 橋本浩一, 熊坂崇, 若槻壮市, 松垣直宏

生化学　84回　ROMBUNNO.1S2A-5-5　2011/09
Publisher: (公社)日本生化学会
ISSN： 0037-1017
SPring-8構造生物学Iビームライン8L41XUの現状

清水伸隆, 牧野正知, 伊藤廉, 長谷川和也, 上野剛, 村上博則, 馬場清喜, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　24th　2011
含水結晶に有効な新しいマウント方法:ポリマーコーティングと湿度調節の組み合わせ

馬場清喜, 星野武司, 伊藤廉, 熊坂崇

日本結晶学会年会講演要旨集　2011　2011
高輝度マイクロビームビームラインBL32XUの現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 二澤宏司, 村上博則, 清水伸隆, 清水伸隆, 熊坂崇, 熊坂崇, 湯本博勝, 湯本博勝, 田中隆次, 高橋直, 高橋直, 竹下邦和, 竹下邦和, 竹内智之, 竹内智之, 大橋治彦, 大橋治彦, 大端通, 大端通, 松下智裕, 松下智裕, 古川行人, 古川行人, 後藤俊治, 後藤俊治, 北村英男, 北村英男, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　24th　2011
GTP結合型M-Ras変異体の二種類の結晶構造から考察される立体構造遷移メカニズム

松本耕祐, 島扶美, 村岡真, 井尻悠一, 市川晋也, 荒木望嗣, 荒木望嗣, 熊坂崇, 田村厚夫, 片岡徹

生化学　2010

ISSN： 0037-1017
枯草菌一般ストレス応答機構の結晶解析

牧野正知, TEH AikHong, 星野武司, 伊藤廉, 熊坂崇

日本農芸化学会大会講演要旨集　2010　2010
蛋白質の凝集抑制剤の探索,抑制機構の解明,及び新規凝集抑制剤の創製

伊藤廉, 伊藤廉, 白木賢太郎, 山口宏, 熊坂崇

日本化学会講演予稿集　90th　(3)　2010

ISSN： 0285-7626
枯草菌の環境ストレス応答に関与する蛋白質群の結晶構造解析に向けた発現・精製・結晶化

伊藤廉, 清水伸隆, 熊坂崇

日本結晶学会年会講演要旨集　2010　2010
タンパク質微小結晶構造解析の現状と展望

平田邦生, 上野剛, 河野能顕, 二澤宏司, 引間孝明, 清水伸隆, 清水伸隆, 熊坂崇, 熊坂崇, 田中隆次, 田中隆次, 高橋直, 高橋直, 竹下邦和, 竹下邦和, 湯本博勝, 湯本博勝, 竹内智之, 竹内智之, 大橋治彦, 大橋治彦, 大端通, 大端通, 松下智裕, 松下智裕, 古川行人, 古川行人, 後藤俊治, 後藤俊治, 北村英男, 山本雅貴

日本蛋白質科学会年会プログラム・要旨集　10th　2010
マイクロビームを用いたタンパク質結晶構造解析の現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 二澤宏司, 清水伸隆, 清水伸隆, 熊坂崇, 熊坂崇, 湯本博勝, 湯本博勝, 田中隆次, 高橋直, 高橋直, 竹下邦和, 竹下邦和, 竹内智之, 竹内智之, 大橋治彦, 大橋治彦, 大端通, 大端通, 松下智裕, 松下智裕, 古川行人, 古川行人, 後藤俊治, 後藤俊治, 北村英男, 山本雅貴

日本結晶学会年会講演要旨集　2010　2010
Extracellular secretion mechanism in Escherichia coli of a recombinant GH family 18 chitinase from alkaliphilic Nocardiopsis sp. F96 : role of signal peptide and mature polypeptide region

ISHIDA Shunsei, KANG Fei, MATSUSHIMA Junya, ENDO Kimiko, MORIGUCHI Manabu, FUKAZAWA Tetsuya, YATSUNAMI Rie, FUKUI Toshiaki, KUMASAKA Takashi, TANAKA Nobuo, NAKAMURA Satoshi

15　(2)　110-111　2009/07/01

ISSN： 1340-9778
GTP結合型Rasの構造遷移における分子メカニズムの解析

井尻悠一, 島扶美, 村岡真, LIAO Jingling, 松本耕祐, 荒木望嗣, 熊坂崇, 田村厚夫, 片岡徹

日本分子生物学会年会講演要旨集　32nd　(Vol.1)　2009
SPring-8構造生物ビームラインの現状

熊坂崇, 長谷川和也, 清水伸隆, 馬場清喜, 水野伸宏, 牧野正知, 星野武司, 伊藤廉, 和田いづみ, 上野剛, 引間孝明, 河野能顕, 平田邦生, 村上博則, 二澤宏司, 前田大輔, 山本雅貴

日本結晶学会年会講演要旨集　2009　2009
SPring-8構造生物学IビームラインBL41XUの現状

清水伸隆, 清水伸隆, 河野能顕, 牧野正知, 長谷川和也, 村上博則, 上野剛, 馬場清喜, 伊藤廉, 二澤宏司, 山本雅貴, 熊坂崇, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　23rd　2009
階層横断生命科学-異分野融合的研究の新展開に向けて-SPring-8構造生物ビームラインの現状

長谷川和也, 清水伸隆, 馬場清喜, 水野伸宏, 牧野正知, 星野武司, 伊藤廉, 和田いづみ, 熊坂崇, 上野剛, 平田邦生, 引間孝明, 河野能顕, 村上博則, 前田大輔, 二澤宏司, 山本雅貴

階層横断生命科学-異分野融合的研究の新展開にむけて理研シンポジウム平成21年　2009
蛋白質凝集抑制剤-蛋白質複合体から見る凝集抑制効果

伊藤廉, 山田好輝, 長谷川和也, 熊坂崇

日本結晶学会年会講演要旨集　2009　2009
SPring-8マイクロビームビームラインBL32XUで可能にするタンパク質微小結晶解析

平田邦生, 二澤宏司, 上野剛, 河野能顕, 引間孝明, 清水伸隆, 清水伸隆, 熊坂崇, 熊坂崇, 田中隆次, 高橋直, 高橋直, 竹下邦和, 竹下邦和, 湯本博勝, 大橋治彦, 大橋治彦, 後藤俊治, 後藤俊治, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　22nd　2009
理研ターゲットタンパクビームラインBL32XUの開発状況

平田邦生, 上野剛, 二澤宏司, 河野能顕, 引間孝明, 清水伸隆, 清水伸隆, 熊坂崇, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 高橋直, 竹下邦和, 竹下邦和, 大橋治彦, 大橋治彦, 大端通, 大端通, 松下智裕, 松下智裕, 古川行人, 古川行人, 後藤俊治, 後藤俊治, 北村英男, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　23rd　2009
タンパク質微小結晶構造解析を実現するSPring-8新規マイクロビームビームラインの開発

平田邦生, 上野剛, 二澤宏司, 河野能顕, 引間孝明, 清水伸隆, 熊坂崇, 清水伸隆, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 竹下邦和, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 高橋直, 竹下邦和, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本結晶学会年会講演要旨集　2009　2009
SPring-8 structural biology beamlines / automatic beamline operation at RIKEN structural genomics beamlines

Go Ueno, Kazuya Hasegawa, Nobuo Okazaki, Raita Hirose, Hisanobu Sakai, Takashi Kumasaka, Takashi Kumasaka, Masaki Yamamoto, Masaki Yamamoto

AIP Conference Proceedings　879　1871-1874　2007/03/26

DOI： 10.1063/1.2436436 　

ISSN： 0094-243X
Automation of the RIKEN structural genomics beamlines at SPring-8

UENO Go, HIROSE Raita, IDA Koh, KANDA Hiroyuki, KUMASAKA Takashi, YAMAMOTO Masaki

19　(2)　83-91　2006/03/31
Publisher: 日本放射光学会
ISSN： 0914-9287
Mechanism of metal activation of human hematopoietic prostaglandin D synthase (vol 10, pg 291, 2003)

T Inoue, D Irikura, N Okazaki, S Kinugasa, H Matsumura, N Uodome, M Yamamoto, T Kumasaka, M Miyano, Y Kai, Y Urade

NATURE STRUCTURAL BIOLOGY　10　(5)　409-409　2003/05

DOI： 10.1038/nsb907 　

ISSN： 1072-8368
Erratum: Mechanism of metal activation of human hematopoietic prostaglandin D synthase (Nature Structural Biology (2003) 10 (291-296)

Inoue, T., Irikura, D., Okazaki, N., Kinugasa, S., Matsumura, H., Uodome, N., Yamamoto, M., Kumasaka, T., Miyano, M., Kai, Y., Urade, Y.

Nature Structural Biology　10　(5)　409　2003/05/01

DOI： 10.1038/nsb0503-409 　

ISSN： 1072-8368
An unexpected gift from fungicide metabolism studies: blasticidin S deaminase (BSD) from Aspergillus terreus Invited

Makoto Kimura, Masaki Yamamoto, Makio Furuichi, Takashi Kumasaka, Isamu Yamaguchi

Progress in Biotechnology　22　(C)　55-60　2002

DOI： 10.1016/S0921-0423(02)80043-0 　

ISSN： 0921-0423
Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBF beta (vol 104, pg 755, 2001)

TH Tahirov, T Inoue-Bungo, H Morii, A Fujikawa, M Sasaki, K Kimura, M Shiina, K Sato, T Kumasaka, M Yamamoto, S Ishii, K Ogata

CELL　105　(2)　291-291　2001/04

ISSN： 0092-8674
Reaction Mechanism and Crystal Structure of 4-α-Glucanotransferase from a Hyperthermophilic Archaeon, Thermococcus litoralis

IMAMURA Hiromi, FUSHINOBU Shinya, YAMAMOTO Masaki, KUMASAKA Takashi, WAKAGI Takayoshi, MATSUZAWA Hiroshi

Journal of applied glycoscience　48　(2)　171-175　2001/04/01
Publisher: The Japanese Society of Applied Glycoscience
DOI： 10.5458/jag.48.171 　

ISSN： 1340-3494

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Thermococcus litoralis 4-α-glucanotransferase (GTase) belongs to family 57 of glycosyl hydro-lases and catalyzes the disproportionation and cycloamylose synthesis reactions. Using 3-ketobutylidene-β-2-chloro-4-nitrophenyl-maltopentaoside (3 KBG 5 CNP) as a donor and glucose as an acceptor, we showed that the disproportionation reaction of 4-α-glucanotransferase involves a Ping-Pong Bi Bi mechanism. Based on this reaction mechanism, we trapped the glycosyl-enzyme intermediate by treating the enzyme with 3 KBG 5 CNP in the absence of an acceptor. MALDITOFMS and PSD analysis of a peptic digest of the intermediate and great decrease in activity of the E 123 Q mutant enzyme indicated that completely conserved Glu 123 was the catalytic amino acid. Next, we have determined the structure of GTase, the first structure of the family 57 of glycosyl hydrolases, at 2.8 Å resolution. The structure of GTase is composed of three domains. N-terminal domain (domain A) contains two catalytic residues and has a novel pseudo-TIM barrel fold. C-terminal domain (domain C) is mainly made of β-strands arranged in two layered β-sheet sandwich. Domain B is located between domains A and C, and consists of α- and 3₁₀-helices. Active site cleft lies between domains A and B. The cleft is partially covered with aromatic residues to form a tunnel-like shape, which probably plays an important role in the formation of large cyclic glucans.
Stractural Biology Topics タバコの自家不和合性に関与するS糖蛋白(S‐RNase)のMAD法を用いたX線結晶構造解析

井田孝, 佐藤衛, 乗岡茂巳, 崎山文夫, 山下栄樹, 山本雅貴, 熊坂崇

構造生物学　15-16　2001
SPring-8におけるダイヤモンドの放射光利用

山本雅貴, 熊坂崇, 石川哲也

ニュ-ダイヤモンド　16　(3)　16-20　2000/07
Publisher: オ-ム社
ISSN： 1340-4792
AML1/CBFA2/PEBP2αBによるDNA認識とCBFβによる活性増強機構の分子構造学的研究

TAHIROV T, 井上泰子, 佐々木元子, 木村一美, 椎名政昭, 佐藤光, 森井尚之, 熊坂崇, 緒方一博

日本分子生物学会年会プログラム・講演要旨集　23rd　2000

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Books and Other Publications 8

生体高分子結晶のX線構造解析: ―実践手法と基礎理論―

竹中章郎, 熊坂, 崇, 近藤, 次郎, 角南, 智子, 茶竹, 俊行, 森下, えら

丸善出版　2022/02/02

ISBN: 4621307061
日本の結晶学(II)ーその輝かしい発展ー

日本結晶学会, 日本の結晶学, I, 出版編集委員会

日本結晶学会　2014/07

ISBN: 9784990386122
タンパク質結晶の最前線 = Frontiers of protein crystals

杉山成

シーエムシー出版　2013/12

ISBN: 9784781309293
バイオ系のための基礎化学問題集 : 生物化学・有機化学・物理化学

梶原将, 三原久和, 湯浅英哉, 小畠英理, 東京工業大学, 東京工業大学大学院生命理工学研究科グローバルCOEプログラム

講談社サイエンティフィク　2008/03

ISBN: 9784061398214
環境とバイオ [バイオ研究のフロンティア 1]

田中信夫

工学図書　2008/03

ISBN: 9784769204855
計算シミュレーションと分析データ解析 [表面分析技術選書]

日本表面科学会

丸善　2008/01

ISBN: 9784621078808
トコトンやさしいタンパク質の本 (B&Tブックス今日からモノ知りシリーズ)

東京工業大学大学院生命理工学研究科, 東京工業大学

日刊工業新聞社　2007/02

ISBN: 9784526058103
光科学研究の最前線2

「光科学研究の最前線」編集委員会, 「光科学研究の最前線2」編集委員会

強光子場科学研究懇談会　2005

ISBN: 4902590018

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Presentations 130

Novel Insights into the Structural Perturbation Induced by the Oncogenic Mutations, Q61L and Q61H, in Ras State 1

Shigeyuki Matsumoto, Haruka Taniguchi-Tamura, Mitsugu Araki, Takashi Kawamura, Ryo Miyamoto, Chiemi Tsuda, Yasushi Okuno, Fumi Shima, Takashi Kumasaka, Tohru Kataoka

BIOPHYSICAL JOURNAL　2020/02
SPring-8タンパク結晶ビームラインにおける自動データ収集システムの現状

平田邦生, 河野能顕, 上野剛, 山下恵太郎, 山下恵太郎, 坂井直樹, 馬場清喜, 水野伸宏, 仲村勇樹, 村上博則, 長谷川和也, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2020
理研構造ゲノムビームラインI&IIの現状

上野剛, 仲村勇樹, 奥村英夫, 伊藤翔, 水野伸宏, 水野伸宏, 引間孝明, 平田邦生, 河野能顕, 村上博則, 馬場清喜, 馬場清喜, 増永拓也, 長谷川和也, 長谷川和也, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2020
SACLA,SPring-8並びにNMRを用いた低分子量Gタンパク質RasのGTP加水分解過程における動的構造解析

佐伯茉帆, 槇野義輝, 松本篤幸, 河村高志, 南後恵理子, 熊坂崇, 島扶美

日本分子生物学会年会プログラム・要旨集(Web)　2020
微小結晶を利用したRas caged-GTP時分割測定の試み

河村高志, 槇野義輝, 長谷川和也, 中根崇智, 馬場清喜, 南後恵理子, 南後恵理子, 田中里枝, 田中里枝, 岩田想, 岩田想, 島扶美, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2020
Redox dependent conformational change of the [2Fe-2S] ferredoxin revealed by ultrahigh resolution X-ray crystallography

OHNISHI Yusuke, TANAKA Hideaki, OKUMURA Hideo, BABA Kiyoki, KAWANO Yoshiaki, KUMASAKA Takashi, TESHIMA Kezo, IKEGAMI Takahisa, IKEGAMI Takahisa, AGO Hideo, UENO Go, MURAKAMI Hironori, YAMASHITA Keitaro, HIRATA Kunio, YAMAMOTO Masaki, KURISU Genji

日本化学会春季年会講演予稿集(CD-ROM)　2020
Structural basis for conformational change of the topaquinone cofactor during the catalytic reaction of bacterial copper amine oxidase

Toshihide Okajima, Takeshi Murakawa, Seiki Baba, Satoshi Kanagawa, Hideyuki Hayashi, Takato Yano, Takashi Kumasaka, Katsuyuki Tanizawa

Protein Science　2019/09
タンパク質結晶におけるX線の動力学的回折の初観測

鈴木凌, 小泉晴比古, 平野馨一, 熊坂崇, 小島謙一, 橘勝

応用物理学会春季学術講演会講演予稿集(CD-ROM)　2019/02/25
理研構造ゲノムビームラインI&IIの現状

上野剛, 仲村勇樹, 奥村英夫, 伊藤翔, 水野伸宏, 水野伸宏, 引間孝明, 平田邦生, 河野能顕, 村上博則, 馬場清喜, 馬場清喜, 増永拓也, 長谷川和也, 長谷川和也, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2019
藍藻由来フェレドキシンの[2Fe-2S]クラスター還元に起因する構造変化の段階的可視化

大西裕介, 田中秀明, 奥村英夫, 馬場清喜, 河野能顕, 熊坂崇, 栗栖源嗣

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2019
LCP結晶から効率よくデータ収集を行う手法開発

平田邦生, 河野能顕, 上野剛, 山下恵太郎, 村上博則, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2019
銅含有アミン酸化酵素触媒機構の“in crystallo“熱力学的解析

村川武志, 馬場清喜, 河野能顕, 林秀行, 矢野貴人, 熊坂崇, 山本雅貴, 谷澤克行, 岡島俊英

日本細胞生物学会大会(Web)　2019
Conformational changes of ferredoxin from Cyanobacteria induced by redox of [2Fe2S] cluster

OHNISHI Yusuke, TANAKA Hideaki, OKUMURA Hideo, BABA Kiyoki, KAWANO Yoshiaki, KUMASAKA Takashi, TESHIMA Kezo, IKEGAMI Takahisa, KURISU Genji

日本化学会春季年会講演予稿集(CD-ROM)　2019
高分解能の結晶構造解析により解明された還元に起因する藍藻由来フェレドキシンの構造変化

大西裕介, 田中秀明, 奥村英夫, 馬場清喜, 河野能顕, 熊坂崇, 栗栖源嗣

日本結晶学会年会講演要旨集　2018/11/01
Present status of SPring-8 macromolecular crystallography beamlines

Hideo Okumura, Kazuya Hasegawa, Seiki Baba, Nobuhiro Mizuno, Hironori Murakami, Takashi Kumasaka, Kunio Hirata, Go Ueno, Masaki Yamamoto

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　2018/08
酸化型フェレドキシンの精密な結晶構造解析に向けた,X線損傷の分光学的評価

大西裕介, 田中秀明, 奥村英夫, 馬場清喜, 河野能顕, 熊坂崇, 栗栖源嗣

日本化学会春季年会講演予稿集(CD-ROM)　2018/03/06
理研構造ゲノムビームラインI&IIの現状

上野剛, 仲村勇樹, 奥村英夫, 伊藤翔, 水野伸宏, 水野伸宏, 引間孝明, 平田邦生, 山下恵太郎, 河野能顕, 村上博則, 馬場清喜, 馬場清喜, 長谷川和也, 長谷川和也, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2018
生体分子モーターが力を発生させているところを見る静的・動的X線結晶構造解析による哺乳類F₁‐ATPaseの回転力発生機構の分析

鈴木俊治, 鈴木俊治, 鈴木俊治, 飯田直也, 平田邦生, 山下栄樹, 馬場清喜, 熊坂崇, 遠藤斗志也, 久堀徹, 吉田賢右, 野地博行

日本生体エネルギー研究会討論会講演要旨集　2017/12/05
SPring‐8 BL38B1の高性能化と利用技術開発

馬場清喜, 奥村英夫, 仲村勇樹, 水野伸宏, 長谷川和也, 河野能顕, 上野剛, 梶原堅太郎, 木村滋, 鈴木凌, 橘勝, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2017/11/23
酸化型フェレドキシン結晶のX線回折実験における還元損傷の確認と評価

大西裕介, 田中秀明, 奥村英夫, 馬場清喜, 河野能顕, 熊坂崇, 栗栖源嗣

日本結晶学会年会講演要旨集　2017/11/23
Observation of dynamical effect on protein crystals in rocking curve measurements

Suzuki Ryo, Murata Hidenobu, Koizumi Haruhiko, Hirano Keiichi, Sugiyama Hiroshi, Kumasaka Takashi, Kojima Kenichi, Tachibana Masaru

Meeting Abstracts of the Physical Society of Japan　2017
理研構造ゲノムビームラインI&IIの現状

上野剛, 仲村勇樹, 奥村英夫, 河野能顕, 水野伸宏, 水野伸宏, 村上博則, 馬場清喜, 馬場清喜, 引間孝明, 長谷川和也, 長谷川和也, 平田邦生, 山下恵太郎, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2017
SPring-8MXBLオンライン顕微分光装置の開発

河野能顕, 奥村英夫, 上野剛, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2017
微小結晶構造解析ビームラインBL32XUの現状

平田邦生, 平田邦生, 河野能顕, 山下恵太郎, 上野剛, 長谷川和也, 長谷川和也, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2017
PXビームラインにおける回折データ自動処理・構造決定システムの開発

山下恵太郎, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム(Web)　2017
Fixed target serial crystallography at SACLA

Masaki Yamamoto, Hideo Ago, Kunio Hirata, Keitaro Yamashita, Go Ueno, Minoru Kubo, Seiki Baba, Kazuya Hasegawa, Takashi Kumasaka, Atsuhiro Shimada, Kyoko Shinzawa-Itoh, Tomitake Tsukihara, Shinya Yoshikawa, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　2017
Development of data collections of SPring-8 MX beamlines

Nobuhiro Mizuno, Kazuya Hasegawa, Seiki Baba, Hideo Okumura, Nipawan Nuemket, Hironori Murakami, Yuki Nakamura, Masaki Yamamoto, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　2017
高エネルギX線を利用した休止酸化型チトクロム酸化酵素の低損傷構造解析

上野剛, 島田敦広, 山下栄樹, 長谷川和也, 熊坂崇, 伊藤(新澤, 恭子, 吉川信也, 月原冨武, 月原冨武, 山本雅貴

日本結晶学会年会講演要旨集　2016/11/17
SPring‐8 MXBLオンライン顕微分光測定装置の開発

奥村英夫, 河野能顕, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2016/11/17
X線自由電子レーザーを用いた,ポンプ・プローブ法によるチトクロム酸化酵素の時分割結晶構造解析

波多野啓太, 島田敦広, 宮本朱梨, 馬場清喜, 山下恵太郎, 久保稔, 吾郷日出夫, 平田邦生, 上野剛, 村上博則, 山本雅貴, 熊坂崇, 山下栄樹, 小倉尚志, 伊藤(新澤)恭子, 月原冨武, 月原冨武, 吉川信也

日本蛋白質科学会年会プログラム・要旨集　2016/05/19
SPring‐8MXBLオンライン顕微分光測定装置の開発

奥村英夫, 河野能顕, 熊坂崇, 山本雅貴

日本蛋白質科学会年会プログラム・要旨集　2016/05/19
深紫外レーザータンパク質結晶加工機の性能評価

松本直記, 松本直記, 河野能顕, 吾郷日出夫, 吾郷日出夫, 馬場清喜, 上野剛, 平田邦生, 山下恵太郎, 熊坂崇, 山本雅貴, 山本雅貴

日本蛋白質科学会年会プログラム・要旨集　2016/05/19
回折データ自動収集・処理システムZooによる微小結晶を用いた高難度タンパク質構造解析の効率化

山下恵太郎, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

日本蛋白質科学会年会プログラム・要旨集　2016/05/19
理研構造ゲノムビームラインI&IIの現状

上野剛, 仲村勇樹, 村上博則, 水野伸宏, 水野伸宏, 馬場清喜, 馬場清喜, 奥村英夫, 長谷川和也, 長谷川和也, 引間孝明, 平田邦生, 山下恵太郎, 河野能顕, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2016/01/09
SPring‐8 MXBL顕微分光測定装置の開発

奥村英夫, 河野能顕, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2016/01/09
微小結晶からの回折データ自動収集システムの開発

平田邦生, 上野剛, 山下恵太郎, 河野能顕, 長谷川和也, 長谷川和也, 熊坂崇, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2016/01/09
微小結晶のための回折データ自動処理システムの開発

山下恵太郎, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2016/01/09
X線自由電子レーザーを用いたチトクロム酸化酵素の時分割構造解析から明らかとなった,銅イオンへの配位子結合によって制御されるプロトンポンプ経路の閉鎖メカニズム

島田敦広, 波多野啓太, 宮本朱梨, 伊藤(新澤, 恭子, 久保稔, 馬場清喜, 熊坂崇, 山本雅貴, 吾郷日出夫, 平田邦生, 山下恵太郎, 山下栄樹, 上野剛, 吉川信也, 月原冨武, 月原冨武

日本生化学会大会(Web)　2016
SPring‐8タンパク質結晶解析ビームラインBL41XUの現状

長谷川和也, 奥村英夫, 馬場清喜, 水野伸宏, 村上博則, 平田邦生, 山下恵太郎, 上野剛, 吾郷日出夫, 中津亨, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2015/10/17
シリアル結晶学における重原子誘導体を用いた位相決定

山下恵太郎, 潘東青, 長谷川和也, 菅原道泰, 村井智洋, 小段篤史, 溝端栄一, 鈴木守, 鈴木守, 桝田哲哉, 桝田哲哉, 平田邦生, 加藤博章, 加藤博章, 吾郷日出夫, 熊坂崇, 山本雅貴, 中津亨, 中津亨

日本結晶学会年会講演要旨集　2015/10
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 東浦彰史, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2015/01/10
生体高分子結晶回折データ自動処理システムの開発

山下恵太郎, 吉村政人, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 水野伸宏, 引間孝明, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2015/01/10
Ligand mutagenesis of TthNEET, a thermophile homolog of mitoNEET

Toshio Iwasaki, Emi Hagiuda, Risako Fukazawa, Yoko Hayashi-Iwasaki, Tairo Oshima, Kazuya Hasegawa, Takashi Kumasaka

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY　2014/08
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 東浦彰史, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2014/01/11
深紫外レーザーを用いたタンパク質結晶加工機の現状

河野能顕, 引間孝明, 山下恵太郎, 松本直記, 平田邦生, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2014
高フラックス微小ビームを用いたタンパク質微小結晶構造解析の新展開

平田邦生, 河野能顕, 山下恵太郎, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2014
SHIKA:回折データ収集のための微小結晶探索効率化ソフトウェアの開発

山下恵太郎, 平田邦生, 河野能顕, 上野剛, 長谷川和也, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2014
微小タンパク質結晶自動凍結システムの開発

引間孝明, 村上博則, 河野能顕, 上野剛, 平田邦生, 水野伸宏, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2013/10/12
深紫外レーザーを用いたタンパク質結晶加工機の開発

河野能顕, 引間孝明, 平田邦生, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2013/10/12
Binding of Vitamin B6 to Aromatic Amino Acid Surface Areas Increases the Solubility of Keratin

ITO Len, KAZUMORI Hazime, MIZUNO Sayaka, INAMI Sachiko, BABA Seiki, KUMASAKA Takashi, KAMIKADO Junichiro

2013/03/01
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)8L44XUの現状

山下栄樹, 東浦彰史, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2013/01/12
構造生物学IビームラインBL41XUの現状と高度化

長谷川和也, 奥村英夫, 馬場清喜, 水野伸宏, 宮野菜央, 平田邦生, 河野能顕, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2013/01/12
ビセニスタチン生合成における糖転移酵素VinCの結晶構造解析

南後恵理子, 南篤志, 沼倉真理緒, 熊坂崇, 江口正

日本農芸化学会大会講演要旨集(Web)　2013
タンパク質微小結晶の迅速・高精度構造解析に向けた技術開発

平田邦生, 河野能顕, 上野剛, 村上博則, 長谷川和也, 奥村英夫, 引間孝明, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2012/10/25
SPring‐8共用PXビームラインの現状と高度化

長谷川和也, 馬場清喜, 水野伸宏, 奥村英夫, 宮野菜央, 平田邦生, 河野能顕, 山本雅貴, 熊坂崇

日本結晶学会年会講演要旨集　2012/10/25
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 梅名泰史, 東浦彰史, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2012/01/06
タンパク質微小結晶自動凍結装置の開発

引間孝明, 橋本浩一, 村上博則, 河野能顕, 上野剛, 平田邦生, 南後恵理子, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2012/01/06
理研ターゲットタンパクビームラインBL32XUの現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 南後恵理子, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2012/01/06
ハイスループット,リモート測定に対応したWebベースの分散型アプリケーションLeafPieの開発

岡崎伸生, 山田悠介, 平田邦生, 玉田太郎, 栗原和男, 山田貢, 熊坂崇, 山本雅貴, 若槻壮市, 黒木良太

PFシンポジウム要旨集　2012
ターゲットタンパクプログラムに向けた放射光ビームライン開発

山本雅貴, 平田邦生, 河野能顕, 橋本浩一, 熊坂崇, 若槻壮市, 松垣直宏

生化学　2011/09
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 鈴木守, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2011/01/07
高輝度マイクロビームビームラインBL32XUの現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 二澤宏司, 村上博則, 清水伸隆, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 竹下邦和, 竹内智之, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2011/01/07
タンパク質試料結晶の放射線損傷とうまく付き合うために

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 南後恵理子, 長谷川和也, 奥村英夫, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2011
メタン生成古細菌由来イソペンテニル二リン酸異性化酵素の構造解析

星野武司, 南後恵理子, 馬場清喜, 江口正, 熊坂崇

日本化学会講演予稿集　2011
内分泌撹乱物質ビスフェノールAによるプロテインジスルフィドイソメラーゼの構造変化とbb’ドメインの結晶化

奥村正樹, 橋本翔子, 伊藤廉, 縄田万里奈, 油谷克英, 芝野智久, 志波公平, 熊坂崇, 今岡進, 山口宏

日本結晶学会年会講演要旨集　2011
タンパク質微小結晶構造解析の現状と展望

平田邦生, 上野剛, 河野能顕, 二澤宏司, 引間孝明, 清水伸隆, 熊坂崇, 田中隆次, 高橋直, 竹下邦和, 湯本博勝, 竹内智之, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本蛋白質科学会年会プログラム・要旨集　2010/05/15
SPring‐8阪大蛋白研ビームラインBL44XUの現状

山下栄樹, 鈴木守, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本結晶学会年会講演要旨集　2010
蛋白質凍結結晶自動サンプルチェンジャーSPACEの高度化

村上博則, 上野剛, 平田邦生, 河野能顕, 橋本浩一, 清水伸隆, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2010
マイクロビームを用いたタンパク質結晶構造解析の現状

平田邦生, 河野能顕, 橋本浩一, 上野剛, 引間孝明, 村上博則, 二澤宏司, 清水伸隆, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 竹下邦和, 竹内智之, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本結晶学会年会講演要旨集　2010
長いHisタグ伸長鎖をつけて結晶化した超好熱菌古細菌Rieskeフェレドキシンの構造・変異酵素解析

鴻巣麻子, 長谷川和也, 熊坂崇, 大森大二郎, 漆山秋雄, 岩崎俊雄

生化学　2010
メタン生成古細菌由来イソペンテニル二リン酸異性化酵素の構造解析

星野武司, 南後恵理子, 馬場清喜, 江口正, 熊坂崇

日本結晶学会年会講演要旨集　2010
2P024 Evaluation of Radiation Damage in Protein Crystal Studied by UV-Visible Spectroscopy(The 48th Annual Meeting of the Biophysical Society of Japan)

Shimizu Nobutaka, Shimizu Tetsuya, Baba Seiki, Hasegawa Kazuya, Yamamoto Masaki, Kumasaka Takashi

Seibutsu Butsuri　2010
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 吉村政人, 鈴木守, 長谷川和也, 古川行人, 大畑通, 熊坂崇, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009/12/10
理研ターゲットタンパクビームラインBL32XUの開発状況

平田邦生, 上野剛, 二澤宏司, 河野能顕, 引間孝明, 清水伸隆, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 竹下邦和, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009/12/10
SPring‐8構造生物学ビームライン/理研構造ゲノムビームラインI&II(BL26B1&B2)の現状

上野剛, 村上博則, 平田邦生, 引間孝明, 二澤宏司, 河野能顕, 前田大輔, 長谷川和也, 馬場清喜, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009/12/10
SPring‐8構造生物学IビームラインBL41XUの現状

清水伸隆, 河野能顕, 牧野正知, 長谷川和也, 村上博則, 上野剛, 馬場清喜, 伊藤廉, 二澤宏司, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009/12/10
SPring‐8生体超分子複合体構造解析ビームライン(大阪大学蛋白質研究所)BL44XUの現状

山下栄樹, 鈴木守, 吉村政人, 長谷川和也, 熊坂崇, 古川行人, 大端通, 上野剛, 山本雅貴, 吉川信也, 月原冨武, 中川敦史

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
タンパク質微小結晶構造解析を実現するSPring‐8新規マイクロビームビームラインの開発

平田邦生, 上野剛, 二澤宏司, 河野能顕, 引間孝明, 清水伸隆, 熊坂崇, 湯本博勝, 田中隆次, 高橋直, 竹下邦和, 大橋治彦, 大端通, 松下智裕, 古川行人, 後藤俊治, 北村英男, 山本雅貴

日本結晶学会年会講演要旨集　2009
階層横断生命科学―異分野融合的研究の新展開に向けて―SPring‐8構造生物ビームラインの現状

長谷川和也, 清水伸隆, 馬場清喜, 水野伸宏, 牧野正知, 星野武司, 伊藤廉, 和田いづみ, 熊坂崇, 上野剛, 平田邦生, 引間孝明, 河野能顕, 村上博則, 前田大輔, 二澤宏司, 山本雅貴

階層横断生命科学-異分野融合的研究の新展開にむけて理研シンポジウム平成21年　2009
SPring‐8構造生物ビームラインの現状

熊坂崇, 長谷川和也, 清水伸隆, 馬場清喜, 水野伸宏, 牧野正知, 星野武司, 伊藤廉, 和田いづみ, 上野剛, 引間孝明, 河野能顕, 平田邦生, 村上博則, 二澤宏司, 前田大輔, 山本雅貴

日本結晶学会年会講演要旨集　2009
SPring‐8分光器の安定化対策

山崎裕史, 清水康宏, 清水伸隆, 河野能顕, 河本正秀, 三浦孝紀, 仙波泰徳, 熊坂崇, 山本雅貴, 大橋治彦, 後藤俊治

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
SPring‐8 BL41XUにおける分光器の安定化対策

清水康宏, 山崎裕史, 清水伸隆, 河野能顕, 河本正秀, 三浦孝紀, 仙波泰徳, 熊坂崇, 山本雅貴, 大橋治彦, 後藤俊治

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
SPring‐8マイクロビームビームラインBL32XUで可能にするタンパク質微小結晶解析

平田邦生, 二澤宏司, 上野剛, 河野能顕, 引間孝明, 清水伸隆, 熊坂崇, 田中隆次, 高橋直, 竹下邦和, 湯本博勝, 大橋治彦, 後藤俊治, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
SPring‐8構造生物学ビームライン/CMOS検出器を用いた回折強度データ測定

長谷川和也, 平田邦生, 清水伸隆, 河野能顕, 熊坂崇, 山本雅貴

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
SPring‐8構造生物学 I ビームラインBL41XUの現状

清水伸隆, 河野能顕, 河本正秀, 長谷川和也, 上野剛, 平田邦生, 大端通, 古川行人, 工藤統吾, 馬場清喜, 清水哲哉, 二澤宏司, 山本雅貴, 熊坂崇

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
必須アミノ酸生合成経路におけるβ-脱炭酸脱水素酵素-阻害剤複合体構造解析

南後恵理子, 南後恵理子, 山本崇史, 熊坂崇, 江口正

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2009
27 Inhibitor Design of Decarboxylating Dehydrogenases(Oral Presentation)

Eguchi Tadashi, Yamamoto Takashi, Nango Eriko, Kumasaka Takashi

Symposium on the Chemistry of Natural Products, symposium papers　2008/09/01

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Homoisocitrate dehydrogenase (HICDH) and 3-isopropylmalate dehydrogenase (IPMDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. HICDH is involved in the α-aminoadipate pathway of L-lysine biosynthesis in higher fungi such as yeast and human pathogenic fungi. This enzyme catalyzes the oxidative decarboxylation of homoisocitrate into 2-ketoadipate using NAD^+ as a coenzyme. IPMDH is a key enzyme in L-leucine biosynthesis of microorganism and plants, and catalyzes the NAD^+ dependent oxidative decarboxylation of the substrate 3-isopropylmalate to 2-oxoisocaproate. Since L-lysine and L-leucine are essential amino acids for animal, these enzymes are considered to be a potential target for new antifungal and antimicrobial agents. Firstly, we designed and synthesized a series of aza-, oxa-, and thia-analogues of homoisocitrate as a potential inhibitor for HICDH as shown Fig. 3. Among them, thia-analogue showed a strong competitive inhibitory activity as K_i=97nM toward HICDH derived from Saccharomyces cerevisiae. Kinetic studies suggested that the formation of the keto-enolate intermediate played an important role in the inhibition. Based on this result, we also synthesized a series of aza-, oxa-, and thia-analogues as an inhibitor for IPMDH. As a result, thia-analogue was found to be a strong competitive inhibitor (K_i=64nM) toward IPMDH derived from Thermus thermophilus. In addition, T. thermophilus IPMDH-inhibitor-NAD^+ crystals were obtained and the structure showed that the product from thia-analogue inhibitor exited in the active site.
1S6-6 Two novel beamlines to achieve protein micro-crystallography(1S6 Cutting edge of protein crystallography with synchrotron radiation,The 46th Annual Meeting of the Biophysical Society of Japan)

Hirata Kunio, Goto Shunji, Kitamura Hideo, Yamamoto Masaki, Matsugaki Naohiro, Yamada Yusuke, Hiraki Masahiko, Igarashi Noriyuki, Yamamoto Shigeru, Tsuchiya Kimichika, Shioya Tatsuro, Nisawa Atsushi, Maezawa Hideki, Asaoka Seiji, Miyauchi Hiroshi, Tahara Toshihiro, Tanimoto Yasunori, Wakatsuki Soichi, Ueno Go, Shimizu Nobutaka, Kumasaka Takashi, Tanaka Takashi, Takahashi Sunao, Takeshita Kunikazu, Ohashi Haruhiko

Seibutsu Butsuri　2008
IPR beamline for macromolecular assemblies at SPring-8

Eiki Yamashita, Masato Yoshimura, Mamoru Suzuki, Takashi Kumasaka, Masaki Yamamoto, Shinya Yoshikawa, Tomitake Tsukihara, Atsushi Nakagawa

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　2008
3S5-1 Technological developments for Synchrotron X-ray Crystallographic Analysis Targeting Proteins Difficult to Solve Their Structures(3S5 Development of Protein Production and Structural Analysis technologies in the Targeted Proteins Research Program,The 46th Annual Meeting of the Biophysical Society of Japan)

Kumasaka Takashi

Seibutsu Butsuri　2008
SPring‐8生体超分子複合体構造解析ビームライン(BL44XU)の現状

山下栄樹, 吉村政人, 鈴木守, 熊坂崇, 山本雅貴, 吉川信也, 中川敦史, 月原冨武

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2007/12/20
SPring‐8構造生物学ビームライン/メールインデータ測定システムとその応用

OKAZAKI NOBUO, HASEGAWA KAZUYA, UENO TAKESHI, MURAKAMI HIRONORI, BABA KIYOKI, KUMASAKA TAKASHI, YAMAMOTO MASATAKA

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2007/12/20
SPring‐8構造生物学ビームライン/ビームラインの自動化

UENO TAKESHI, MURAKAMI HIRONORI, HIRATA KUNIO, HASEGAWA KAZUYA, OKAZAKI NOBUO, BABA KIYOKI, KUMASAKA TAKASHI, YAMAMOTO MASATAKA

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2007/12/20
SPring‐8構造生物学ビームライン/共用ビームラインBL38B1,BL41XUの現状

BABA KIYOKI, SHIMIZU NOBUTAKA, KAWAMOTO MASAHIDE, HASEGAWA KAZUYA, OKAZAKI NOBUO, UENO TAKESHI, MURAKAMI HIRONORI, KUMASAKA TAKASHI, YAMAMOTO MASATAKA

日本放射光学会年会・放射光科学合同シンポジウム予稿集　2007/12/20
佐賀LS・BL15におけるタンパク質結晶のX線回折実験

河本正秀, 清水伸隆, 馬場清喜, 平田邦生, 石地耕太朗, 隅谷和嗣, 岡島敏浩, 本島浩之, 渡邉啓一, 熊坂崇, 山本雅貴

日本結晶学会年会講演要旨集　2007
SPring-8 structural biology beamlines/automatic beamline operation at RIKEN Structural Genomics Beamlines

Go Ueno, Kazuya Hasegawa, Nobuo Okazaki, Raita Hirose, Hisanobu Sakai, Takashi Kumasaka, Masaki Yamamoto

SYNCHROTRON RADIATION INSTRUMENTATION, PTS 1 AND 2　2007

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RIKEN Structural Genomics Bean-dines (BL26B1 & BL26B2) at SPring-8 have been constructed for high throughput protein crystallography. The beamline operation is automated cooperating with the sample changer robot. The operation software provides a centralized control utilizing the client and server architecture. The sample management system with the networked database has been implemented to accept dry-shipped crystals from distant users.
SPring‐8構造生物学ビームラインにおけるメールインデータ測定

OKAZAKI NOBUO, HASEGAWA KAZUYA, UENO TSUYOSHI, MURAKAMI HIRONORI, BABA SEIKI, KUMASAKA TAKASHI, YAMAMOTO MASAKI

日本結晶学会年会講演要旨集　2007
モデル系としての[2Fe-2S]タンパク質の結晶構造と¹⁵N HYSCORE解析

鴻巣麻子, 岩崎俊雄, 大森大二郎, DIKANOV Sergei A., 内山琢郎, 熊坂崇, 熊坂崇

生化学　2007
1P067 The micro-focus beamline to open the new field of protein micro-crystallography(Proteins-functions, methodology, and protein enigineering,Oral Presentations)

Kunio Hirata, Atsushi Nisawa, Go Ueno, Nobutaka Shimizu, Takashi Kumasaka, Masaki Yamamoto

Seibutsu Butsuri　2007
Characterization of domain-shuffled and/or amino-acid-substituted beta-1,3-glucanase from alkaliphilic actinomycete

Koizumi Naoya, Maeda Kiyoe, Isoda Yuya, Masuda Sumiko, Fibriansah Guntur, Kumasaka Takashi, Yatsunami Rie, Fukui Toshiaki, Nakamura Satoshi

Proceeding of Annual/Fall Meetings of the Japan Petroleum Institute　2007
1P022 Present Status of Protein Micro-crystallography at SPring-8(Proteins-structure and structure-function relationship,Oral Presentations)

Shimizu N., Kawamoto M., Hasegawa K, Kitamura Y., Ebihara A., Ueno G., Hirata K, Shimizu T., Nisawa A., Kuramitsu S., Kumasaka T., Yamamoto M.

Seibutsu Butsuri　2007
Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site

Toshio Iwasaki, Asako Kounosu, Daijiro Ohmori, Takashi Kumasaka

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　2006/10

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In place of the Rieske [2Fe-2S] cluster, an archetypal mononuclear iron site has rationally been designed into a hyperthermophilic archaeal Rieske [2Fe-2S] protein (sulredoxin) from Sulfolobus tokodaii by three residue replacements with reference to the Pyrococcus furiosus rubredoxin sequence. The resulting sulredoxin variant, SDX-triple (H44I/A45C/H64C), has been purified and crystallized by the hanging-drop vapour-diffusion method using 65%(v/v) 2-methyl-2,4-pentanediol, 0.025 M citric acid and 0.075 M sodium acetate trihydrate pH 4.3. The crystals diffract to 1.63 angstrom resolution and belong to the triclinic space group P1, with unit-cell parameters a = 43.56, b = 76.54, c = 80.28 angstrom, alpha = 88.12, beta = 78.82, gamma = 73.46 degrees. The asymmetric unit contains eight protein molecules.
Functional analysis of the signal peptide of chitinase F1 from alkaliphilic Nocardiopsis sp. strain F96

YATSUNAMI Rie, MATSUSHIMA Junya, ENDO Kimiko, MORIGUCHI Manabu, FUKAZAWA Tetsuya, FUKUI Toshiaki, MATSUI Tsutomu, SATO Takao, KUMASAKA Takashi, TANAKA Nobuo, NAKAMURA Satoshi

2006/07/01
Catalytic Mechanism of Family 18 Chitinase from Alkaliphilic Nocardiopsis sp. Strain F96 and Its Extracellular Secretion in Escherichia coli

MATSUSHIMA J., ENDO K., MORIGUCHI M., FUKAZAWA T., YATSUNAMI R., FUKUI T., MATSUI T., SATO T., KUMASAKA T., TANAKA N., NAKAMURA S.

2005/07/01
Structural Basis of leukotriene B-4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase Catalytic Mechanism and a Possible SH3-binding Loop

T Hori, T Yokomizo, H Ago, M Sugahara, G Ueno, M Yamamoto, T Kumasaka, T Shimizu, M Miyano

FASEB JOURNAL　2004/05
Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain (vol 278, pg 48162, 2003)

T Kaneko, T Kumasaka, T Ganbe, T Sato, K Mayazawa, N Katamura, N Tanaka

JOURNAL OF BIOLOGICAL CHEMISTRY　2004/02
Crystal structure of the hyperthermophilic archael sulredoxin variant, CLCA, having the unique Rieske [2Fe-2S] cluster environment without any disulfide linkage

UCHIYAMA T, KOUNOSU A, SATO T, IWASAKI T, KUMASAKA T

生化学　2004
Mechanism of metal activation of human hematopoietic prostaglandin D synthase (vol 10, pg 291, 2003)

T Inoue, D Irikura, N Okazaki, S Kinugasa, H Matsumura, N Uodome, M Yamamoto, T Kumasaka, M Miyano, Y Kai, Y Urade

NATURE STRUCTURAL BIOLOGY　2003/05
糖質加水分解酵素のバレル構造: ファミリー42と57のX線結晶構造解析

伏信進矢, 日高将文, 今村博臣, 山本雅貴, 熊坂崇, 松沢洋, 若木高善, 祥雲弘文

日本農芸化学会大会講演要旨集　2003
A small deletion of the flexible C-terminal region significantly affects substrate binding and catalytic efficiency in blasticidin S deaminase from Aspergillus terreus (BSD)

KIMURA Makoto, FURUICHI Makio, YAMAMOTO Masaki, KUMASAKA Takashi, MIZUNO Hiroshi, MIYANO Masashi, YAMAGUCHI Isamu

2001/02/22
リンゴ銀葉病菌の生産するエンドポリガラクツロナーゼIのX線結晶構造解析 (第二報)

清水哲哉, 中津亨, 山本雅貴, 熊坂崇, 宮入一夫, 奥野智旦, 加藤博章

日本農芸化学会誌,75,180　2001
Crystal structure of rhodopsin: A G-protein-coupled receptor

K Palczewski, T Kumasaka, T Hori, CA Behnke, H Motoshima, BA Fox, IL Trong, DC Teller, T Okada, RE Stenkamp, M Yamamoto, M Miyano

BIOPHYSICAL JOURNAL　2001/01
The ligand recogunition mechanism of Blasticidin S deaminase(BSD)

Furuichi M., Kimura M., Yamamoto M., Kumasaka T., Yamashita S., Mizuno H.

Seibutsu Butsuri　2001
AML1/CBFA2/PEBP2αBによるDNA認識とCBFβによる活性増強機構の分子構造学的研究

TAHIROV T, 井上泰子, 佐々木元子, 木村一美, 椎名政昭, 佐藤光, 森井尚之, 熊坂崇, 緒方一博

日本分子生物学会年会プログラム・講演要旨集　2000/11/25
Crystal structure of metalloendopeptidase from Grifola frondosa reveals structural features of a novel metalloendopeptidase family, 'aspzincin', and the mechanism of substrate recognition

T Hori, T Kumasaka, M Yamamoto, T Nonaka, N Tanaka, Y Hashimoto, Z Takio

FASEB JOURNAL　2000/05
1-II-9 L-メチオニンγ-リアーゼの立体構造

稲垣賢二, 田村隆, 田中英彦, 本島浩之, 熊坂崇, 古市真木雄, 山本雅貴, 田中信夫, 江崎信芳, 左右田健次

ビタミン　2000/04/25
Subnanometer mechanical switch revealed in the atomic model of F41 fragment of flagellin

Samatey Fadel, Imada K., Nagashima S., Vonderviszt Ferenz, Kumasaka T., Yamamoto M., Namba K.

Seibutsu Butsuri　2000
プロモーター部位におけるMybとC/EBPとの相互作用の分子構造学的研究

TAHIROV T H, 佐々木元子, 井上泰子, 藤川敦, 森井尚之, 熊坂崇, 山本雅貴, 石井俊輔, 緒方一博

日本分子生物学会年会プログラム・講演要旨集　1999/11/22
SPring‐8における蛋白質結晶構造解析多波長異常分散法に最適化したBL45XU(理研ビームラインI)

熊坂崇, 山本雅貴, 山下栄樹, 森山英明, 植木龍夫

スーパーコンピュータと専用計算機における計算科学講演要旨集　1999/03/16
SPring‐8理研ビームラインに於ける4×4配列型CCD素子X線検出器の評価実験

鈴木昌世, 山本雅貴, 熊坂崇, 佐藤一道, 豊川秀訓, 山下栄樹, 森山英明, 植木龍夫

日本放射光学会年会・放射光科学合同シンポジウム予稿集　1999/01/07
Structure and function of importin-β mutant

Lee Soo Jae, Imamoto Naoko, Sakai Hiroaki, Yamamoto Masaki, Kumasaka Takashi, Yoneda Yoshihiro, Tsukihara Tomitake

Seibutsu Butsuri　1999
理研ビームラインIでのMAD法

熊坂崇, 山本雅貴, 山下栄樹, 森山英明, 植木龍夫

日本結晶学会年会講演要旨集　1998/11
Preliminary X-ray crystallographic study of Thurmus themophilas valyl-tRNA synthetase complexed with a cognale tRNA

Fukai S., Nureki O., Sekine S., Shimada A., Kumasaka T., Yamamoto M., Vassylyev D.G., Yokoyama S.

Biophysics　1998/09/07
理研ビームラインI・蛋白質結晶構造解析ステーション

山本雅貴, 熊坂崇, 山下栄樹, 森山英明, 植木龍夫

日本放射光学会年会・放射光科学合同シンポジウム予稿集　1998/01/09
CCD[4×4]配列型X線検出器システムの特性評価

鈴木昌世, 豊川秀訓, 佐藤一道, 山本雅貴, 熊坂崇, 植木龍夫

日本放射光学会年会・放射光科学合同シンポジウム予稿集　1998/01/09
SPring-8理研構造生物学研究用ビームラインBL45XU I

山本雅貴, 熊坂崇, 中迫雅由, 藤澤哲郎, 鈴木昌世, 植木龍夫

日本結晶学会誌　1996
SPring-8理研構造生物学研究用ビームラインBL-45XU II

熊坂崇, 山本雅貴, 中迫雅由, 鈴木昌世, 植木龍夫

日本結晶学会誌　1996
亜鉛プロテアーゼの低温下における多波長でのデータ収集

熊坂崇, 山本雅貴, 中迫雅由, 田中信夫, 植木龍夫, 山河芳夫, 佐藤保, 岩永貞昭

日本結晶学会誌　1995
ハブ毒H₂-proteinaseの構造精密化

熊坂崇, 山本雅貴, 田中信夫, 山河芳夫, 佐藤保, 佐藤衛, 勝部幸輝, 武谷浩之, 岩永貞昭

日本結晶学会誌　1994
ハブ毒H₂-プロテイナーゼの結晶構造解析

熊坂崇, 山本雅貴, 田中信夫, 山河芳夫, 佐藤保, 佐藤衛, 勝部幸輝, 武谷浩之, 岩永貞昭

日本結晶学会誌　1993

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Industrial Property Rights 7

微小試料用キャピラリー

熊坂崇, 牧野正知, 桑本いづみ, 山本雅貴

Property Type: Patent
結晶の回折測定方法及びそのための回折測定装置

熊坂崇, 馬場清喜, 星野武司

特許5807946

Property Type: Patent
変異型Rasポリペプチドの結晶

片岡徹, 島扶美, 田村厚夫, 熊坂崇

Property Type: Patent
リポカリン型プロスタグランジンD合成酵素の3次元立体構造及びその使用

宮野雅司, 山本雅貴, 熊坂崇, 吾郷日出夫, 裏出良博, 入倉大祐, 有竹浩介

Property Type: Patent
プロスタグランジンD合成酵素の3次元立体構造及びその使用

井上豪, 甲斐泰, 裏出良博, 岡野洋介, 衣笠茂浩, 松村浩由, 入倉大祐, 早石修, 山本雅貴, 熊坂崇, 宮野雅司

特許4071477

Property Type: Patent
サンプルの支持機構

山本雅貴, 熊坂崇

特許3640383

Property Type: Patent
ウシ・ロドプシンの立体構造

宮野雅司, クルジイストフ, パルチェウスキー, 熊坂崇, 堀哲哉, クライグエイ, ベーンケ, 本島浩之, ブライアンエイ, フォックス, イソルデレ, トロング, デイビッド, シーテラー, 岡田哲二, ロナルドイー, ステンカンプ, 山本雅貴

Property Type: Patent

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Research Projects 19

細胞膜受容体の動的構造解析と活性化機構の解明

南後恵理子, 浅田秀基, 保坂俊彰, 清中茂樹, 熊坂崇

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(A)

Institution: 東北大学

2024/04 - 2027/03
Development of fixed target micro-crystallography dedicated to structural dynamics study

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Institution: Institute of Physical and Chemical Research

2019/06 - 2024/03
Investigation of protein structure and signaling molecule in general stress response in Bacillus subtilis

Kumasaka Takashi, Nipawan Nuemket, Omichi Kazuki

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Japan Synchrotron Radiation Research Institute

2016/04/01 - 2019/03/31

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Bacillus subtilis is difficult to sterilize due to the formation of spores that are resistant to heat and dryness, and therefore causes food spoilage and its growth control has become an issue. In this study, we proceeded to elucidate the signal transduction mechanism of proteins responsible for general stress response of Bacillus subtilis by crystallographic analysis. RsbQ / P proteins, involved In the signal transduction of nutrient stress, suggested the contribution of ligand molecules, then here we elucidated the protein-ligand complex structure. The RsbP has a complex structure, suggesting activation by signal transduction inside the molecule, then here we constructed and proposed an entire molecular model by combination of partial crystal structural analysis and X-ray solution scattering. In addition, structural analysis of the proteins involved in this system was also carried out, and some crystals were obtained for proteins involved in the upstream part.
Research on the molecular basis of conformational dynamics of oncogene product Ras for application to the development of its specific inhibitors

shima fumi, KITAHARA Ryou

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (B)

Institution: Kobe University

2014/04/01 - 2017/03/31

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ras proto-oncogene products Ras, is a member of small GTPases, which is frequently activated in a wide variety of human cancers, making them promising anti-cancer drug targets. In the present study, we determined the novel druggable pocket structure of Ras by Synchrotron X-ray crystallography utilizing Humid Air and Glue-coating (HAG) mounting method, which unveiled the molecular basis of conformational transition between the open and closed pocket structures. Molecular Dynamics simulation of the solved structures lead us to a reasonable agreement with experimental observations and the consequent scenarios on the transition. Further, crystal structure analysis of Ras/fragment-compound complex by cross-linking method gave us useful information on the structure-based design of Ras inhibitors.
Structure-function studies of bacterial mitoNEET system

Iwasaki Toshio, KUSANO TERUO, KUMASAKA TAKASHI, IWASAKI HIDEO

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Nippon Medical School

2014/04/01 - 2016/03/31

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MitoNEET is a novel outer-mitochondrial membrane iron-sulfur protein, recently identified as a potential mitochondrial target that binds pioglitazone, an insulin sensitizer for the treatment of type II diabetes. Recently we constructed a null-deletion mutant strain of Thermus thermophilus lacking TthNEET (the thermophile homolog of mitoNEET), and found a “prokaryotic glucose intolerance” for this delta-TthNEET null strain. In this work, we characterized TthNEET mutant proteins and strains with altered [2Fe-2S] cluster redox potentials by X-ray crystallographic and physiological analyses to better understand the structure-function relationships of this class of proteins, and explored the protein interaction network of TthNEET by monitoring the whole-cell global changes of the Thermus protein components, using pulldown assays and two-dimensional gel electrophoresis.
枯草菌一般ストレス応答システムの構造と機能の解析

熊坂崇

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 新学術領域研究(研究領域提案型)

Institution: 公益財団法人高輝度光科学研究センター

2013/04/01 - 2015/03/31

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今年度は以下の３課題に取り組んだ。 1) ストレス応答を抑制するタンパク質ホスファターゼRsbXの構造機能解析：この構造は既に得ていたが、Mnイオン2個を含む活性部位が壊れていた。さらに活性型構造と他のイオンに置き換えた構造解析と活性測定を行って、構造機能相関を調べた。類似構造と比較して特徴的なのは、Mnクラスタの配位子として4つのAsp側鎖に加えて、主鎖のカルボニル酸素2つが存在する点である。後者は易動性のループ構造上にあり、異なる結晶系での解析から3種類の構造が得られた。そのうち2つはMnが1つしか存在しない不活性型構造であり、ループ構造の変化に由来する活性制御機構の存在を示唆する。実際、培地のMn濃度がストレス応答に関わるという報告もあり、この分子機構との関係が示唆され、これらを報文として報告した。 2) 関連タンパク質の調製：巨大分子Stressosome (RsbRS)複合体については、安定した試料調製が可能となり、結晶も得られた。分解能は8 Aと低いが、純度向上と条件検討を継続中である。またその構成成分のRsbSの結晶回折能を向上させ2.9 A分解能のデータを取得、解析中である。RsbQについては、枯草菌による発現と酵素活性の測定により、シグナル分子の同定に迫りつつある。さらに、ストレスシグナルが最終的に伝達されるRNA polymeraseについて調製を行い、結晶化条件のスクリーニングを実施した。 3) タンパク質結晶の新規マウント技術：水分を多く含み脆いタンパク質結晶を安定にＸ線回折測定を行うマウント手法(HAG法)の開発を継続した。特に、RsbQ結晶で良好な結果を与えるが、これは結晶コーティング用高分子の結晶への低浸透性が奏功したと考えられる。これを受けてコーティング剤の最適化を進め、汎用性を高めた。
A new capillary mounting technique for protein microcrystals and its derivatization by xenon

KUMASAKA Takashi, MAKINO Masatomo

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Japan Synchrotron Radiation Research Institute

2011/04/28 - 2015/03/31

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Synchrotron microbeam technology has opened the new window of protein crystallography―enabling us to analyze atomic structures from the microcrystals with the size of ca. 10 um. Such tiny and fragile crystals, however, were difficult to be handled in 2011 when this project has been started. To solve the issue, we developed a mounting technique inspired by a capillary used for microinjection in cell biology. Glass capillary is rigid, therefore it can be made sharper. The fine and tapered capillary, with 15 um diameter at its tip, successfully held and cooled the crystals. The capillary can minimize amount of solvent, leading to the reduction of X-ray scattering noise. Since the capillary is resistant to pressure, it is also used as a gas-derivatization tool. The capillary attached to a screw-type mounting tool can directly connect to the gas-pressurization device. By a simple procedure, the xenon-derivatives of egg-white lysozyme crystals was prepared and phased by X-ray anomalous data.
Structure-function of bacterial mitoNEET homologs

IWASAKI TOSHIO, KUSANO Teruo, KUMASAKA Takashi, IWASAKI Hideo

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Challenging Exploratory Research

Institution: Nippon Medical School

2012/04/01 - 2014/03/31

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MitoNEET is a mammalian mitochondrial outer membrane iron-sulfur protein with a potential pharmacological and clinical target of pioglitazone, an insulin-sensitizer for the treatment of type II diabetes. In this study, we conducted the phenotypal analyses of a deletion strain and several mutant strains of a bacterial mitoNEET homolog (TthNEET) of Thermus thermophilus HB8 in comparison with the wild-type strain, and re-analyzed the available metabolome and microarray datasets of this thermophile. We also obtained the high-resolution X-ray diffraction datasets of mammalian mitoNEET in complex with several drug compounds.
枯草菌一般ストレス応答システムの構造生物学

熊坂崇

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 新学術領域研究(研究領域提案型)

Institution: 公益財団法人高輝度光科学研究センター

2011/04/01 - 2013/03/31

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本研究では原核生物の一般ストレス応答について、未知のシグナル分子の探索と構造に基づく遺伝子改変を表現型で観察するための分子基盤の構築を目標として、枯草菌の情報伝達機構に関わる蛋白質群の構造機能解析を目的とし、次の2点の研究を進めた。1) ストレス応答にかかわる分子複合体構造：環境応答ストレス情報伝達の巨大ハブ分子であるStressosomeを中心とした結晶構造解析による分子活性制御機構，2) 栄養飢餓ストレス分子の同定とその作用機序：未知の飢餓シグナル分子のリレーによる情報伝達機構につき、分子同定と構造に基づくマルチドメインタンパク質の活性化機構．「1)ストレス応答に関わる分子複合体構造の解明」について、Stressosomeを構成するキナーゼRsbTとその基質でSTASファミリに属するRsbSの機能解析と結晶化を行った。その結果、RsbTだけでなくRsbSの機能としてNTP分解活性を有することが明らかとなり、これを受けてRsbS-NTP複合体の結晶化を進めた結果、従来の六方晶系の結晶に加え、新たに斜方晶系で3.0Aの回折能をもつ結晶を得た。現在、ハロゲンで修飾したNTPなどを用いた誘導体結晶の回折データ測定と位相決定に取り組んでおり、並行して得られたNTP活性測定の結果と合わせて、RsbSの構造機能相関の解明を進めている。一方「2)栄養飢餓ストレス分子の同定とその作用機序の解明」については、RsbPの活性化機構を構造の見地から解明するため、我々が解析した非活性型のホスファターゼドメイン構造に基づき、活性化に関与することが報告されているN末端部のヘリックスを伸長した活性型タンパク質の発現系の構築と結晶化を進めた。得られたタンパク質は活性を持たず、また結晶は得られたものが十分な回折能を与えず、解析には至らなかった。活性化に関わる部位の厳密な同定が必要と考えている。
Anti-cancer drug design targeting a novel tertiary structure of ras oncogene product

SHIMA Fumi, KUMASAKA Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Kobe University

2008 - 2010

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GTP-bound form of ras oncogene product Ras exhibits dynamic equilibrium between two interconverting conformations, "inactive" state 1 and "active" state 2. Based on a novel tertiary structure of Ras-GTP, we have performed in silico and in vitro screening for low molecular weight compounds which inhibit Ras function. Consequently, we have succeeded in identification of several hit compounds which specifically bind and inhibit Ras function in vitro and in vivo.
Structural Biology on Signal Transduction of Stress Response in Bacillus subtilis

KUMASAKA Takashi

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Japan Synchrotron Radiation Research Institute

2007 - 2008
Exploring heterologous overexpression system and modular assembly of archaeal metalloenzyme complexes

IWASAKI Toshio, KUMASAKA Takashi, OHMORI Daijiro

Offer Organization: Japan Society for the Promotion of Science

System: Grants-in-Aid for Scientific Research

Category: Grant-in-Aid for Scientific Research (C)

Institution: Nippon Medical School

2006 - 2008
枯草菌ストレス応答系のシグナル伝達機構に関する構造研究

熊坂崇

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 若手研究(B)

Institution: 東京工業大学

2005 - 2006

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今年度は、当初計画に基づき、枯草菌のストレス応答系の蛋白質について、発現系構築および結晶化条件の検索を中心として行った。昨年度大腸菌での高発現系を構築したSigB蛋白質については、認識DNA配列あるいはAgonistでRsbW蛋白質との複合体の結晶化スクリーニングを行ったが、これまでのところで結晶は得られていない。さらにAntagonistであるRsbV蛋白質の大腸菌での発現系を構築し、高純度で精製試料が得られた。収量が少なく結晶化には至らなかったものの今後、RsbW-RsbV複合体を目指して結晶化条件検索を進める予定である。既に我々が構造解析を行ったエネルギーストレス系に属するRsbQは、RsbPへシグナルを伝達する重要な蛋白質である。この加水分解酵素がストレスシグナル分子を分解して、RsbPのPer-Arnt-Simドメインに受け渡し、Phosphatase活性を上昇させる。得られた分子構造から、この未知シグナル分子は疎水性低分子であると考えられたため、種々の候補分子についてエステラーゼ活性の測定を行った。その結果、ややK_iが高いものの、フェノール類と短鎖のカルボン酸からなるエステルが有力な候補であることを見出した。これを受けて、RsbPのオリゴマーを乖離させるものと考えられるシグナル分子の探索を引き続き進めている。さらに、環境ストレス系においては、RsbR, RsbXの大腸菌発現系の作成に成功し、結晶化実験を試みた。その結果、RsbXにおいて、1.3Å分解能の結晶を得ることに成功した。現在、得られたX線回折データを用いて構造解析を進めるとともに、結晶化に関する報文を準備している。
新規構造を持つ担子菌由来亜鉛プロテアーゼの結晶構造解析

熊坂崇

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 奨励研究(A)

Institution: 理化学研究所

2000 - 2001

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プロテアーゼは生体の内外でたんぱく質を分解するという、生命に必須な機能を持つ重要なたんぱく質ファミリーである。なかでも、亜鉛プロテアーゼは、至適pHが中性から弱アルカリ性にあるのが特徴で、一次構造の相同性や亜鉛の配位構造などによって分類されている。本研究の担子菌由来の亜鉛プロテアーゼは、舞茸子実体中に豊富に存在し、抽出が比較的容易なため、その応用も検討されているたんぱく質である。また、Aspzincinと呼ばれるファミリーに属しているが、その構造は解析されておらず、亜鉛配位子も確定していなかった。本研究ではこの分子の構造構築原理ならびに基質認識機構を解明する目的で、3次元構造を解明することを目指した。破砕した舞茸子実体からカラムクロマトグラフィーにより試料を抽出し、結晶化を行った結果、4種類の結晶系で結晶を得ることができた。これらの試料を基に、大型放射光施設SPring-8の理研ビームラインIで多波長異常分散法を行うことにより、良好な電子密度図を得ることができ、分子構造を解明することができた。得られた構造には、4本のストランドと1本のヘリックスからなる上部ドメインと4本のヘリックスからなる下部ドメインがあり、それをつなぐ長いヘリックスが存在している。亜鉛配位子は新規なモチーフHEXXH+GTXDXXYGであった。リジン残基のアミノ末端側を切断するこの酵素の基質認識には、亜鉛イオンの傍らに設けられたS1'ポケットが重要な役割を果たしていることを示唆した。このポケットの深さによって、同じ極性を持つアルギニン残基が入っても、亜鉛との位置関係によって反応中間体を安定に保持することができない。また、このポケットのふたの部分にあたる位置にチロシン残基が存在していることがわかった。この残基は長い側鎖のリジンの認識や、反応中間体の安定に寄与するものであることを明らかにした。
微生物のストレス応答機構の構造生物学 Competitive

System: その他の研究制度

2001 -
タンパク質結晶学の方法論 Competitive

System: その他の研究制度

1996 -

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結晶学における位相問題や高精度データ収集に関して放射光を利用した手法や技術の開発を行っている。
タンパク質の構造機能相関 Competitive

System: その他の研究制度

1996 -

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主としてX線結晶解析法を用い、種々のタンパク質の立体構造を解明して、その機能との相関を明らかにする。枯草菌のストレス応答タンパク質や亜鉛タンパク質、糖分解酵素、ウイルス関連タンパク質、膜タンパク質など幅広い対象について研究を進めている。
Methodology of Protein Crystallography Competitive

System: The Other Research Programs

1996 -
Structural and functional relationships of proteins Competitive

System: The Other Research Programs

1996 -

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