RIKEN SPring-8 Center SR Life Science Instrumentation Team
Team Leader: Masaki Yamamoto (Ph.D.)
Research Summary

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
Keywords
- 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
Feb. 9, 2018
A light touch for enzyme analysisDec. 15, 2017
How bacteria avoid poisoning themselvesSep. 22, 2017
Watching enzymes inhaleFeb. 6, 2015
Shining a gentle light on photosynthesisJul. 18, 2014
X-ray studies without the damage
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