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RIKEN SPring-8 Center Life Science Research Infrastructure Group

Group Director: Masaki Yamamoto (Ph.D.)

Research Summary

Masaki  Yamamoto(Ph.D.)

Macromolecular crystallography (MX) of difficult target such as membrane proteins has been successfully achieved by using bright light source of SPring-8. To emphasize the application of structural analysis such as better understanding of life and drug discovery, our group advance the research facilities (SPring-8 and SACLA) for MX or small angle X-ray scattering (Bio-SAXS). Moreover, we facilitate the use of electron cryo-microscopy (cryo-EM) to expect synergy on structural biology activity in addition to those techniques using X-ray. Our group tackle with new structural life science for complex structure-function analysis by combining such state-of-the-art analytical techniques.

Main Research Fields

  • Biology

Related Research Fields

  • Chemistry
  • Engineering
  • Biological Sciences
  • Agricultural Sciences
  • Medicine, Dentistry & Pharmacy
  • Structural biochemistry
  • Biophysics
  • Drug development chemistry

Keywords

  • Structural life Science
  • Structural Biology
  • Correlative Structural Analysis
  • Drug Discovery
  • Structural Dynamics

Selected Publications

  • 1. Takizawa, N., Ogura, Y., Fujita, Y., Noda, T., Shigematsu, H., Hayashi, T., Kurokawa, K.:
    "Local structural changes of the influenza A virus ribonucleoprotein complex by single mutations in the specific residues involved in efficient genome packaging"
    Virology 531, 126-140, (2019)
  • 2. Hanawa-Suetsugu, K., Itoh, Y., Ab Fatah, M., Nishimura, T., Takemura, K., Takeshita, K., Kubota, S., Miyazaki, N., Wan Mohamad Noor, WNI., Inaba, T., Nguyen, NTH., Hamada-Nakahara, S., Oono-Yakura, K., Tachikawa, M., Iwasaki, K., Kohda, D., Yamamoto, M., Kitao, A., Shimada, A. and Suetsugu, S.:
    "Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7"
    Nature Communications10, 4763 (2019)
  • 3. Shigematsu, H., Imasaki, T., Doki, C., Sumi, T., Aoki, M., Uchikubo-Kamo, T., Sakamoto, A., Tokuraku, K., Shirouzu, M. and Nitta, R.:
    "Structural insight into microtubule stabilization and kinesin inhibition by Tau family MAPs"
    Journal of Cell Biology 217 (12), 4155-4163 (2018)
  • 4. Yamamoto, M., Hirata, K., Yamashita, K., Hasegawa, K., Ueno, G., Ago, H., and Kumasaka, T.:
    "Protein microcrystallography using synchrotron radiation"
    IUCrJ 4 (5), 529-539 (2017)
  • 5. M Suga, F Akita, M Sugahara, M Kubo, Y Nakajima, T Nakane, K Yamashita, Y Umena, M Nakabayashi, T Yamane, T Nakano, M Suzuk, T Masuda, S Inoue, T Kimura, T Nomura, S Yonekura, L-J Yu, T Sakamoto, T Motomura, J-H Chen, Y Kato1, T Noguchi, K Tono, Y Joti, T Kameshima, T Hatsui, E Nango, R Tanaka, H Naitow, Y Matsuura, A Yamashita, M Yamamoto, O Nureki, M Yabashi, T Ishikawa, S Iwata, J-R Shen.:
    "Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL"
    Nature 543(7643):131-135 (2017)
  • 6. Matsumoto, S., Miyano, N., Baba, S., Liao, J., Kawamura, T., Tsuda, C., Takeda A,, Yamamoto, M., Kumasaka, T., Kataoka, T. and Shima, F.:
    "Molecular Mechanism for Conformational Dynamics of Ras・GTP Elucidated from In-Situ Structural Transition in Crystal"
    Scientific Report 6, 25931 (2016)
  • 7. Deng, D, Sun, PC, Yan, CY, Ke, M, Jiang, X, Xiong, L, Ren, WL, Hirata, K, Yamamoto, M, Fan, SL and Yan, N.:
    "Molecular basis of ligand recognition and transport by glucose transporters"
    Nature 526 (7573), 391-396.(2015)
  • 8. Tanabe, H, Fujii, Y, Okada-Iwabu, M, Iwabu, M, Nakamura, Y, Hosaka, T, Motoyama, K, Ikeda, M, Wakiyama, M, Terada, T, Ohsawa, N, Hato, M, Ogasawara, S, Hino, T, Murata, T, Iwata, S, Hirata, K, Kawano, Y, Yamamoto, M, Kimura-Someya, T, Shirouzu, M, Yamauchi, T, Kadowaki, T, and Yokoyama,S.:
    "Crystal structures of the human adiponectin receptors"
    Nature 520 (7547), 312-316 (2015)
  • 9. Shima, F, Yoshikawa, Y., Ye, M., Araki, M, Matsumoto, S., Liao, JL., Hu, LZ., Sugimoto, T ., Ijiri, Y., Takeda, A., Nishiyama, Y., Sato, C., Muraoka, S.,Tamura, A., Osoda, T., Tsuda, K., Miyakawa, T., Fukunishi, H., Shimada, J., Kumasaka, T., Yamamoto, M., Kataoka, T.:
    "In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction"
    Proc. Nat. Acad. Sci the USA 110, 8182-8187 (2013)
  • 10. Smith, JL., Fischetti RF. and Yamamoto, M.:
    "Micro-crystallography comes of age"
    Current Opinion in Structural Biology 22, 602-612 (2012)

Related Links

Lab Members

Principal investigator

Masaki Yamamoto
Group Director

Core members

Hideki Shigematsu
Research Scientist
Naoki Sakai
Research Scientist
Kohei Takeshita
Research Scientist
Hiroaki Matsuura
Postdoctoral Researcher

Contact Information

Structural Biology Facility,
1-1-1 Kouto, Sayo-cho,
Sayo-gun, Hyogo,
679-5148 Japan
Tel: +81-(0)791-58-2839
Fax: +81-(0)791-58-2834
Email: yamamoto [at] riken.jp

Organization

SR Life Science Instrumentation Team
Masaki Yamamoto (Ph.D.)

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