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. 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).