SUZUKI, Hirofumi

写真a

Affiliation

Research Council (Research Organization), Research Organization for Nano & Life Innovation

Job title

Junior Researcher(Assistant Professor)

Education 【 display / non-display

  • 1989.04
    -
    1993.03

    Aichi Institute of technology   Information Network Engineering  

Degree 【 display / non-display

  • 名古屋大学   博士(理学)

Research Experience 【 display / non-display

  • 2018.10
    -
    Now

    Waseda University   School of Advanced Science and Engineering   Junior Researcher/Lecturrer

  • 2006.04
    -
    2018.09

    Osaka University   Institute for Protein Research   Specially Appointed Researcher / Specially Appointed Assistant Prof.

  • 2005.10
    -
    2006.05

    JST   CREST   researcher

  • 2004.03
    -
    2005.09

    Biomolecular Engineering Research Institute   Group for Structure Analysis   researcher

  • 2002.12
    -
    2004.02

    ICORP   Dynamic Nanomachine   researcher

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Professional Memberships 【 display / non-display

  •  
     
     

    PROTEIN SCIENCE SOCIETY OF JAPAN

  •  
     
     

    THE BIOPHYSICAL SOCIETY OF JAPAN

 

Research Areas 【 display / non-display

  • Structural biochemistry   Electron microscopy

  • Structural biochemistry   Structure databases

  • Theory of informatics

Research Interests 【 display / non-display

  • electron microscopy

  • structural biology

  • bioinformatics

Papers 【 display / non-display

  • Protein Data Bank: The single global archive for 3D macromolecular structure data

    Burley, Stephen K. Berman, Helen M. Bhikadiya, Charmi Bi, Chunxiao Chen, Li Costanzo, Luigi Di Christie, Cole Duarte, Jose M. Dutta, Shuchismita Feng, Zukang Ghosh, Sutapa Goodsell, David S. Green, Rachel Kramer Guranovic, Vladimir Guzenko, Dmytro Hudson, Brian P. Liang, Yuhe Lowe, Robert Peisach, Ezra Periskova, Irina Randle, Chris Rose, Alexander Sekharan, Monica Shao, Chenghua Tao, Yi Ping Valasatava, Yana Voigt, Maria Westbrook, John Young, Jasmine Zardecki, Christine Zhuravleva, Marina Kurisu, Genji Nakamura, Haruki Kengaku, Yumiko Cho, Hasumi Sato, Junko Kim, Ju Yaen Ikegawa, Yasuyo Nakagawa, Atsushi Yamashita, Reiko Kudou, Takahiro Bekker, Gert Jan Suzuki, Hirofumi Iwata, Takeshi Yokochi, Masashi Kobayashi, Naohiro Fujiwara, Toshimichi Velankar, Sameer Kleywegt, Gerard J. Anyango, Stephen Armstrong, David R. Berrisford, John M. Conroy, Matthew J. Dana, Jose M. Deshpande, Mandar Gane, Paul Gáborová, Romana Gupta, Deepti Gutmanas, Aleksandras Koča, Jaroslav Mak, Lora Mir, Saqib Mukhopadhyay, Abhik Nadzirin, Nurul Nair, Sreenath Patwardhan, Ardan Paysan-Lafosse, Typhaine Pravda, Lukas Salih, Osman Sehnal, David Varadi, Mihaly Vǎreková, Radka Markley, John L. Hoch, Jeffrey C. Romero, Pedro R. Baskaran, Kumaran Maziuk, Dimitri Ulrich, Eldon L. Wedell, Jonathan R. Yao, Hongyang Livny, Miron Ioannidis, Yannis E

    Nucleic Acids Research   47 ( D1 ) D520 - D528  2019  [Refereed]

     View Summary

    The Protein Data Bank (PDB) is the single global archive of experimentally determined threedimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible ww- PDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

    DOI PubMed

  • Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins

    Mika Sakamoto, Hirofumi Suzuki, Kei Yura

    Biophysics and Physicobiology   16 ( 0 ) 68 - 79  2019  [Refereed]

     View Summary

    Transport of small molecules across the cell membrane is a crucial biological mechanism for the maintenance of the cell activity. ABC transporter family is a huge group in the transporter membrane proteins and actively transports the substrates using the energy derived from ATP hydrolysis. In humans, there are 48 distinct genes for ABC transporters. A variation of a single amino acid in the amino acid sequence of ABC transporter has been known to be linked with certain disease. The mechanism of the onset of the disease by the variation is, however, still unclear. Recent progress in the method to measure the structures of huge membrane proteins has enabled determination of the 3D structures of ABC transporters and the accumulation of coordinate data of ABC transporter has enabled us to obtain clues for the onset of the disease caused by a single variation of amino acid residue. We compared the structures of ABC transporter in apo and ATP-binding forms and found a possible conformation shift around pivot-like residues in the transmembrane domains. When this conformation change in ABC transporter and the location of pathogenic variation were compared, we found a reasonable match between the two, explaining the onset of the disease by the variation. They likely cause impairment of the pivot-like movement, weakening of ATP binding and weakening of membrane surface interactions. These findings will give a new interpretation of the variations on ABC transporter genes and pave a way to analyse the effect of variation on protein structure and function.

    DOI PubMed

  • New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

    Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura

    Protein Science   27 ( 1 ) 95 - 102  2017.09  [Refereed]

     View Summary

    The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.

    DOI PubMed

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

    Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura

    Nucleic Acids Research   45 ( D1 ) D282 - D288  2016.10  [Refereed]

     View Summary

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

    DOI PubMed

  • Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

    Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura

    NUCLEIC ACIDS RESEARCH   40 ( D1 ) D453 - D460  2012.01  [Refereed]

     View Summary

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

    DOI PubMed

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Books and Other Publications 【 display / non-display

  • 見てわかる構造生命科学:生命科学研究へのタンパク質構造の利用

    中村春木( Part: Joint author, Structure-3 スライディング・クランプ, Structure-11 リボソーム, Structure-12 シャペロニン, Structure-13 プロテアソーム)

    化学同人  2014.03

Works 【 display / non-display

  • 万見プライム

    鈴木博文  Web Service 

     View Summary

    生き物の分子の立体構造を見ながら、生物学を楽しみ学ぶためのサービス(教育向けコンテンツ)

  • Omokage search

    Hirofumi SUZUKI  Web Service 

     View Summary

    shape similarity search service for 3D structures of macromolecules.

  • Yorodumi

    Hirofumi SUZUKI  Web Service 

     View Summary

    browser for structure data from EMDB, PDB, SASBDB, etc.

  • EM Navigator

    Hirofumi SUZUKI  Web Service 

     View Summary

    3D electron microscopy data browser

Other 【 display / non-display

  • サイエンスアゴラ PDBj/阪大蛋白研 ブース運営

  • One per household "Proteins in Motion!"

     View Summary

    http://www.mext.go.jp/b_menu/houdou/26/03/1346105.htm