1. Home
  2. Research
  3. Centers & Labs
  4. RIKEN SPring-8 Center
  5. Advanced Photon Technology Division

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


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

Selected Publications

  • 1. Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, H., Ogasawara, S., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H., Gopalasingam, C., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada, R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Ishii, Y., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., and Shintani, Y.:
    "Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases"
    Nature Communications 13, 7591 (2022).
  • 2. Gerle, C., Kishikawa, J.I., Yamaguchi, T., Nakanishi, A., Çoruh, O., Makino, F., Miyata, T., Kawamoto, A., Yokoyama, K., Namba, K., and Kurisu, G.:
    "Structures of multisubunit membrane complexes with the CRYO ARM 200"
    Microscopy 71(5), 249-261 (2022).
  • 3. Yoshimi, K., Takeshita, K., Kodera, N., Shibumura, S., Yamauchi, Y., Omatsu, M., Umeda, K., Kunihiro, Y., Yamamoto, M., and Mashimo, T.:
    "Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3"
    Nature communications 13(1), 4917 (2022).
  • 4. Gopalasingam, C.C., and Hasnain, S.S.:
    "Frontiers in metalloprotein crystallography and cryogenic electron microscopy"
    Current Opinion in Structural Biology 75, 102420 (2022).
  • 5. Kutsukawa, R., Imaizumi, R., Suenaga-Hiromori, M., Takeshita, K., Sakai, N., Misawa, S., Yamamoto, M., Yamaguchi, H., Miyagi-Inoue, Y., Waki, T., Kataoka, K., Nakayama, T., Yamashita, S., and Takahashi, S.:
    "Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination"
    The FEBS Journal 289(15), (2022).
  • 6. Tanaka, S., Morita, M., Yamagishi, T., Madapally, H.V., Hayashida, K., Khandelia, H., Gerle, C., Shigematsu, H., Oshima, A., and Abe, K.:
    "Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump"
    Journal of Medicinal Chemistry 65(11), 7843-7853 (2022).
  • 7. Baba, S., Matsuura, H., Kawamura, T., Sakai, N., Nakamura, Y., Kawano, Y., Mizuno, N., Kumasaka, T., Yamamoto, M., and Hirata, K.:
    "Guidelines for de novo phasing using multiple small-wedge data collection"
    Journal of Synchrotron Radiation 28, 1284-1295 (2021).
  • 8. Tojo, S., Zhang, Z., Matsui, H., Tahara, M., Ikeguchi, M., Kochi, M., Kamada, M., Shigematsu, H., Tsutsumi, A., Adachi, N., Shibata, T., Yamamoto, M., Kikkawa, M., Senda, T., Isobe, Y., Ohto, U., and Shimizu T.:
    "Structural analysis reveals TLR7 dynamics underlying antagonism"
    Nature Communications 11(1), 5204 (2020).
  • 9. Gopalasingam, C.C., Johnson, R.M., Chiduza, G.N., Tosha, T., Yamamoto, M., Shiro, Y., Antonyuk, S.V., Muench, S.P., and Hasnain, S.S.:
    "Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo–electron microscopy"
    Science Advances 5(8), eaax1803 (2019).
  • 10. 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).

Related Links

Lab Members

Principal investigator

Masaki Yamamoto
Group Director

Core members

Kohei Takeshita
Research Scientist
Christoph Gerle
Research Scientist
Hiroaki Matsuura
Postdoctoral Researcher
Chai Gopalasingam
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


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