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RIKEN SPring-8 Center Biostructural Mechanism Group

Group Director: Koji Yonekura (Ph.D.)

Research Summary

Koji  Yonekura(Ph.D.)

We have been studying high-resolution structures of biological macromolecular complexes, membrane proteins and complex organic molecules by cryo-electron microscopy (EM) and also developing technologies for this aim. Single particle analysis is applied to larger proteins that yield good image contrast in vitreous ice. Cryo-electron diffraction is available to undersized crystals of smaller molecules, which are hard to be solved by single particle analysis and to grow to a suitable size for X-ray diffraction even with the synchrotron radiation. Our cryo-EM system can provide data with the world-highest quality in both the applications. By complimentary use of SPring-8 / SACLA, we pursue advanced analyses.

Main Research Fields

  • Biology

Related Research Fields

  • Chemistry
  • Biological Science
  • Physics


  • Cryo-EM
  • High-resolution single particle analysis
  • Electron 3D crystallography, eEFD, 3D ED/ microED
  • Membrane protein
  • Macromolecular complex

Selected Publications

  • 1. Takaba K., Maki-Yonekura S., Inoue I., Tono K., Fukuda Y., Shiratori Y., Peng Y., Morimoto J., Inoue S., Higashino T., Sando S., Hasegawa T., Yabashi M. and Yonekura K.:
    "Comprehensive application of XFEL microcrystallography for challenging targets in various organic compounds"
    J. Am. Chem. Soc. 146, 5872-5882 (2024).
  • 2.Yonekura K., Maki-Yonekura S. and Takaba K.:
    "Applications and limitations of electron 3D crystallography"
    Structure, 31, 1328-1334 (2023).
  • 3.Maki-Yonekura S., Kawakami K., Takaba K., Hamaguchi T. and Yonekura K.:
    "Measurement of charges and chemical bonding in a cryo-EM structure"
    Commun. Chem., 6, 98 (2023).
  • 4.Takaba K., Maki-Yonekura S., Inoue I., Tono K., Hamaguchi T., Kawakami K., Naitow H., Ishikawa T., Yabashi M. and Yonekura K.:
    "Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography"
    Nat. Chem., 15, 491-497 (2023).
  • 5.Aizawa H., Sato T., Maki-Yonekura S., Yonekura K., Takaba K., Hamaguchi T., Minato T. and Yamamoto H. M.:
    "Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect"
    Nat. Commun., 14, 4530 (2023).
  • 6.Hamaguchi T., Maki-Yonekura S., Naitow H., Matsuura Y., Ishikawa T. and Yonekura K.:
    "A new cryo-EM system for single particle analysis"
    J. Structl. Biol. 207: 40-48 (2019).
  • 7.Yonekura K., Ishikawa T. and Maki-Yonekura S.:
    "A new cryo-EM system for electron 3D crystallography"
    J. Structl. Biol. 206: 243-253 (2019).
  • 8.Yonekura K., Kato K., Ogasawara M., Tomita M. and Toyoshima C.:
    "Electron crystallography of ultra-thin 3D protein crystals: atomic model with charges"
    Proc. Natl. Acad. Sci. USA 112: 3368-3373, (2015).
  • 9.Yonekura K., Maki-Yonekura S. and Namba K.:
    "Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy"
    Nature 424, 623-650 (2003).
  • 10.Yonekura K., Maki S., Morgan D. G., DeRosier D.J., Vonderviszt F., Imada K. and Namba K.:
    "The bacterial flagellar cap as the rotary promoter of flagellin self-assembly"
    Science 290: 2148-2152 (2000).

Recent Research Results

Related Links

Lab Members

Principal investigator

Koji Yonekura
Group Director

Core members

Hisashi Naito
Senior Research Scientist
Tasuku Hamaguchi
Research Scientist
Keisuke Kawakami
Research Scientist
Kiyofumi Takaba
Postdoctoral Researcher


Position Deadline
Seeking a few Research Scientists or Postdoctoral Researchers (C21-0301) Open until filled

Contact Information

1-1-1 Kouto, Sayo-cho
Sayo-gun, Hyogo
679-5148 Japan
Email: yone [at] spring8.or.jp