RIKEN SPring-8 Center Biostructural Mechanism Group

Group Director: Koji Yonekura (Ph.D.)

Japanese Page

Research Summary

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).