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RIKEN SPring-8 Center Biostructural Mechanism Group

Group Director: Koji Yonekura (Ph.D.)

Research Summary

Koji  Yonekura(Ph.D.)

There are many huge macromolecular complexes and biological important membrane proteins in living organisms. They are often hard to crystallize because of their size, complexity and heterogeneity. Cryo-electron microscopy (EM) is a suitable method for structural studies of such biological macromolecules, because it can be applied to various forms of samples. By using a newly designed cryo-EM system, we are analyzing conformational changes and charges in working biological molecules. Targets include energizing membrane proteins and macromolecular complexes. We also use X-ray crystallography and coherent X-ray imaging for advanced analyses.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Chemistry
  • Biology
  • Biological Science
  • Physics


  • cryo-electron microscopy
  • X-ray crystallography
  • membrane protein
  • macromolecular complex

Selected Publications

  • 1.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 (2018) 7: e35419. doi: 10.7554/eLife.35419
  • 2.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 (2018) 5: 348 - 353. doi: 10.1107/S2052252518005237
  • 3.Yonekura, K. and Maki-Yonekura, S.:
    "Refinement of cryo-EM structures using scattering factors of charged atoms"
    J. Appl. Cryst. 49, 1517–1523 (2016)
  • 4.Takayama, Y. and Yonekura, K.:
    "Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy"
    Acta Cryst. A, 72, 179-189 (2016).
  • 5.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).
  • 6.Takayama, Y., Maki-Yonekura, S., Oroguchi, T., Nakasako, M. and Yonekura, K.:
    "Signal-enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects"
    Sci. Rep. 5, 8074, doi:10.1038/srep08074 (2015).
  • 7.Yonekura, K., Watanabe, M., Kageyama, Y., Hirata, K., Yamamoto, M. and Maki-Yonekura, S.:
    "Post-transcriptional regulator Hfq binds catalase HPII: crystal structure of the complex"
    PLOS ONE 8, e78216, doi:10.1371/journal.pone.0078216 (2013).
  • 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

Contact Information

1-1-1 Kouto, Sayo-cho
Sayo-gun, Hyogo
679-5148 Japan

Email: yone [at] spring8.or.jp