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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

Keywords

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

Selected Publications

  • 1. 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).
  • 2. Yonekura K., Ishikawa T. and Maki-Yonekura S.:
    "A new cryo-EM system for electron 3D crystallography"
    J. Structl. Biol. 206: 243-253 (2019).
  • 3. Guzman-Afonso C., Hong Y.-L., Colaux H., Iijima H., Saitow A., Fukumura T., Aoyama Y., Motoki S., Oikawa T., Yamazaki T., Yonekura K. and Nishiyama Y.:
    "Understanding hydrogen bonding structure of molecular crystals by electron-and NMR-nanocrystallography"
    Nat. Commun. 10: 3537 (2019).
  • 4. Maki-Yonekura S., Matsuoka R., Yamashita, Y., Shimizu H., Tanaka M., Iwabuki F. and Yonekura K.:
    "Hexameric and pentameric complexes of the ExbBD energizer in the Ton system"
    eLife 7: e35419. doi: 10.7554/eLife.35419 (2018).
  • 5. Yonekura K., Matsuoka R., Yamashita Y., Yamane T., Ikeguchi M., Kidera A. and Maki-Yonekura S.:
    "Ionic scattering factors of atoms composing biological molecules"
    IUCrJ 5: 348 - 353. doi: 10.1107/S2052252518005237 (2018).
  • 6. Yonekura K. and Maki-Yonekura S.:
    "Refinement of cryo-EM structures using scattering factors of charged atoms"
    J. Appl. Cryst. 49: 1517?1523 (2016).
  • 7. 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).
  • 8. Maki-Yonekura S., Yonekura K. and Namba K.:
    "Conformational change of flagellin for polymorphic supercoiling of the flagellar filament"
    Nat. Struct. Mol. Biol. 17: 417-422 (2010).
  • 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

Contact Information

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

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