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RIKEN SPring-8 Center SR Life Science Instrumentation Team

Team Leader: Masaki Yamamoto (Ph.D.)

Research Summary

Masaki  Yamamoto(Ph.D.)

SR Life Science Instrumentation Team has mission of research and development of new technologies for structural biology and beamlines at SPring-8 site. Our mission includes technologies on instrumentation of beamline optics, experimental station, sample handling and X-ray detectors, and methodologies on data collection and structure determination by using SPring-8 or SACLA. Moreover, our team is responsible for the operation of four RIKEN structural biology beamlines (BL32XU, BL26B1&B2, and BL38B1). The methodology development on damage-free crystallography and X-ray coherent diffraction cryo-imaging based on ultra-bright and short pulse beam of SACLA for life science research is going on.

Main Research Fields

  • Biology

Related Research Fields

  • Engineering
  • Agricultural Sciences
  • Medicine, Dentistry & Pharmacy
  • Structural biochemistry
  • Biophysics
  • Quantum beam science


  • Synchrotron Radiation Beamline
  • Macromolecular Crystallography
  • Bio-SAXS
  • Coherent Diffraction Imaging

Selected Publications

  • 1. Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T. Hirata, K., Umena, Y., Yonekura, S., Yu, L.-J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K., Yamamoto, M., Ago, H. and Shen, J.-R.:
    "An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser"
    Science, 366, 334-338 (2019)
  • 2. Liu, X., Xu, X., Hilger, D., Aschauer, P., Tiemann, JKS., Du, Y., Liu, H., Hirata, K., Sun, X., Guixa-Gonzalez, R., Mathiesen, JM., Hildebrand, PW. & Kobilka, BK.:
    "Structural Insights into the Process of GPCR-G Protein Complex Formation"
    Cell 177, 1243-1251 (2019)
  • 3. Basu, S., Olieric, V., Leonarski, F., Matsugaki, N., Kawano, Y., Takashi, T., Huang, C.-Y., Yamada, Y., Vera, L., Olieric, N., Basquin, J., Wojdyla, J. A., Bunk, O., Diederichs, K., Yamamoto, M. & Wang, M.:
    "Long-wavelength native-SAD phasing: opportunities and challenges"
    IUCrJ 6, 373-386 (2019)
  • 4. Hirata, K., Yamashita, K., Ueno. G., Kawano Y., Hasegawa, K., Kumasaka, T., Yamamoto, M.:
    "ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography"
    Acta Crystallographica Section D 75, 138-150 (2019)
  • 5. Yamashita, K., Hirata, K., Yamamoto, M.:
    "KAMO: towards automated data processing for microcrystals."
    Acta Crystallographica Section D 74, 441-449 (2018)
  • 6. Hasegawa, K., Yamashita, K., Murai, T. Nuemket,N., Hirata, K., Ueno, G., Ago, H., Nakatsu, T., Kumasaka, T., and Yamamoto. M.:
    "Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography"
    Journal of Synchrotron Radiation 24 (1), 29-41 (2017)
  • 7. Kobayashi, A., Sekiguchi, Y., Takayama, Y., Oroguchi, T., Shirahama, K., Torizuka, Y., Manoda, M., Nakasako, M. and Yamamoto, M.:
    "TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA."
    Review of Scientific Instruments 87, 053109 (2016)
  • 8. Keitaro Yamashita, K., Pan, D., Okuda, T., Sugahara, M., Kodan, A., Yamaguchi, T., Murai, T., Gomi, K., Kajiyama, N., Mizohata, E., Suzuki, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Park, J., Song, C., Hatsui, T., Yabashi, M., Iwata, S., Kato, H., Ago, H., Yamamoto, M. and Nakatsu, T.:
    "An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography."
    Scientific Reports 5, 14017 (2015)
  • 9. Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., Shimizu, T., Yamashita, K., Yamamoto, M., Ago, H., and Shen J.R.:
    "Native structure of photosystem II at 1.95A resolution viewed by femtosecond X-ray pulses"
    Nature 517, 99-103 (2015).
  • 10. Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J. R., *Yoshikawa, S. and Ago, H.:
    "Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL"
    Nature Methods 11, 734-746 (2014)

Recent Research Results

Related Links

Lab Members

Principal investigator

Masaki Yamamoto
Team Leader

Core members

Hideo Ago
Senior Research Scientist
Hiroshi Sugimoto
Senior Research Scientist
Takehiko Tosha
Senior Research Scientist
Yoshiaki Kawano
Senior Technical Scientist
Go Ueno
Senior Technical Scientist
Kunio Hirata
Senior Technical Scientist
Takaaki Hikima
Research Scientist
Amane Kobayashi
Special 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