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.
Abe, S., Tanaka, J., Kojima, M., Kanamaru, S., Hirata, K., Yamashita, K., Kobayashi, A., and Ueno, T.:
"Cell-free protein crystallization for nanocrystal structure determination"
Scientific reports 12, 16031 (2022). - 2.
Imaizumi, Y., Takanuki, K., Miyake, T., Takemoto, M., Hirata, K., Hirose, M., Oi, R., Kobayashi, T., Miyoshi, K., Aruga, R., Yokoyama, T., Katagiri, S., Matsuura, H., Iwasaki, K., Kato, T., Kaneko, M.K., Kato, Y., Tajiri, M., Akashi, S., Nureki, O., Hizukuri, Y., Akiyama, Y., and Nogi, T.:
"Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP"
Science Advances 8, eabp9011 (2022). - 3.
Kwon, H., Basran, J., Pathak, C., Hussain, M., Freeman, S.L., Fielding, A.J., Bailey, A.J., Stefanou, N., Sparkes, H.A., Tosha, T., Yamashita, K., Hirata, K., Murakami, H., Ueno, G., Ago, H., Tono, K., Yamamoto, M., Sawai, H., Shiro, Y., Sugimoto, H., Raven, E., and Moody, P.C.E.:
"XFEL Crystal Structures of Peroxidase Compound II"
Angewandte Chemie International Edition 60 (26) ,14578-14585 (2021). - 4.
Maeki, M., Ito, S., Takeda, R., Ueno, G., Ishida, A., Tani, H., Yamamoto, M., and Tokeshi, M.:
"Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis"
Chemical Science 11, 9072-9087 (2020). - 5.
Nakasako, M., Kobayashi, A., Takayama, Y., Asakura, K., Oide, M., Okajima, K., Oroguchi, T., and Yamamoto, M.:
"Methods and application of coherent X-ray diffraction imaging of noncrystalline particles"
Biophysical reviews 12(2), 541-567 (2020). - 6.
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). - 7.
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., and Wang, M.:
"Long-wavelength native-SAD phasing: opportunities and challenges"
IUCrJ 6, 373-386 (2019). - 8.
Hirata, K., Yamashita, K., Ueno. G., Kawano Y., Hasegawa, K., Kumasaka, T., and Yamamoto, M.:
"ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography"
Acta Crystallographica Section D 75, 138-150 (2019). - 9.
Yamashita, K., Hirata, K., and Yamamoto, M.:
"KAMO: towards automated data processing for microcrystals"
Acta Crystallographica Section D 74, 441-449 (2018). - 10.
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).
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
- Yoshiaki Kawano
- Senior Technical Scientist
- Go Ueno
- Senior Technical Scientist
- Kunio Hirata
- Senior Technical Scientist
- Takaaki Hikima
- Research Scientist
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