Yonekura K., Matsuoka R., Yamashita Y., Yamane T., Ikeguchi M., Kidera A. and Maki-Yonekura S.
Ionic scattering factors of atoms that compose biological molecules.
IUCrJ (2018) 5: 348 - 353. doi: 10.1107/S2052252518005237

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

Yonekura K. and Maki-Yonekura S.
Refinement of cryo-EM structures using scattering factors of charged atoms.
J. Appl. Cryst. (2016) 49: 1517-1523.

Nango E., Akiyama S., Maki-Yonekura S., Ashikawa Y., Kusakabe Y., Krayukhina E., Maruno T., Uchiyama S., Nuemket N., Yonekura K., Shimizu M., Atsumi N., Yasui N., Hikima T., Yamamoto M., Kobayashi Y. and Yamashita A.
Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains.
Sci. Rep. (2016) 6: 25745.

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 Crystallogr. A Found Adv. (2016) 72: 179-189.

Oroguchi T., Sekiguchi Y., Kobayashi A., Masaki Y., Fukuda A., Hashimoto S., Nakasako M., Ichikawa Y., Kurumizaka H., Shimizu M., Inui Y., Matsunaga S., Kato T., Namba K., Yamaguchi K., Kuwata K., Kameda H., Fukui N., Kawata Y., Kameshima T., Takayama Y., Yonekura K. and Yamamoto M.
Cryogenic coherent X-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA.
J. Phys. B: At. Mol. Opt. Phys. (2015) 48: 184003.

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 (2015) 112: 3368-3373.

Takayama Y., Maki-Yonekura S., Nakasako M., Oroguchi T. and Yonekura K.
Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects.
Sci. Rep. (2015) 5: 8074. doi:10.1038/srep08074

Xu R., Jiang H., Song C., Huang Z., Rodriguez J. A., Chen C-C., Nam D., Park J., Gallagher-Jones M., Kim S., Kim S., Suzuki A., Takayama Y., Oroguchi T., Takahashi Y., Fan J., Zou Y., Hatsui T., Inubushi Y., Kameshima T., Yonekura K., Tono K., Togashi T., Sato T., Yamamoto M., Nakasako M., Yabashi M., Ishikawa T. and Miao J.
Single shot three-dimensional imaging of high-index-faceted nanocrystals with femtosecond X-ray free electron laser pulses.
Nat. Commun. (2014) 5: 4061.

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 (2013) 8: e78216. doi:10.1371/journal.pone.0078216

Staals, R. H. J., Agari, Y., Maki-Yonekura, S., Zhu, Y., Taylor, D. W., van Duijn, E., Barendregt, A., Vlot, M., Koehorst, J. J., Sakamoto, K., Masuda, A., Dohmae, N., Schaap, P. J., Doudna, J. A., Heck, A. J. R., Yonekura, K., van der Oost, J. and Shinkai, A.
Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus.
Molecular Cell (2013) 52: 135-145.

Nakasako, M., Takayama, Y., Oroguchi, T., Sekiguchi, Y., Kobayashi, A., Shirahama, K., Yamamoto, M., Hikima, T., Yonekura, K., Maki-Yonekura, S., Kohmura, Y., Inubushi, Y., Takahashi, Y., Suzuki, A., Matsunaga, S., Inui, Y., Tono, K., Kameshima, T., Joti, Y. and Hosh, T.
KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging.
Rev. Sci. Instrum. (2013) 84: 093705.

Yonekura, K., Maki-Yonekura, S. and Homma, M.
Structure of the Flagellar Motor Protein Complex PomAB: Implications for the Torque-Generating Conformation.
J. Bacteriol. (2011) 193: 3863-3870.


Williams, T. L., Levy, D. L., Maki-Yonekura, S., Yonekura, K. and Blackburn, E. H.
Characterization of the yeast telomere nucleoprotein core: Rap1 binds independently to each recognition site.
J. Biol. Chem. (2010) 285: 35814-35824.

Maki-Yonekura, S., Yonekura, K. and Namba, K.
Conformational change of flagellin for polymorphic supercoiling of the flagellar filament.
Nat. Struct. Mol. Biol. (2010) 17: 417-422.

Maki-Yonekura, S. and Yonekura, K.
Electron digital imaging towards high-resolution structure analysis of biological macromolecules.
Microsc. Microanal. (2008) 14: 362-369.

Yonekura, K. and Toyoshima, C.
Structure determination of tubular crystals of membrane proteins. IV. Distortion correction and its combined application with real-space averaging and solvent flattening.
Ultramicroscopy (2007) 107: 1141-1158.

Yonekura, K., Braunfeld, M. B., Maki-Yonekura, S. and Agard, D. A.
Electron energy filtering significantly improves amplitude contrast of frozen-hydrated protein at 300 kV.
J. Struct. Biol. (2006) 156: 524-536.

Kitao, A., Yonekura, K., Maki-Yonekura, S., Samatey, F. A., Imada, K. Namba, K. and Go, N.
Switch interactions control energy frustration and multiple flagellar filament structures.
Proc. Natl. Acad. Sci. USA (2006) 103: 4894-4899.

Yonekura, K., Yakushi, T., Atsumi, T., Maki-Yonekura, S., Homma, M. and Namba, K.
Electron cryomicroscopic visualization of PomA/B stator units of the sodium-driven flagellar motor in liposomes.
J. Mol. Biol. (2006) 357: 73-81.

Tanaka, M., Chien, P., Yonekura, K. and Weissman, J. S.
Mechanism of cross-species prion transmission: an infectious conformation compatible with two highly divergent Yeast prion proteins.
Cell (2005) 121: 49-62.

Yonekura, K., Maki-Yonekura, S. and Namba, K.
Building the atomic model for the bacterial flagellar filament by electron cryomicroscopy and image analysis.
Structure (2005) 13: 407-412.

Yonekura, K. and Namba, K.
Motile structure: Cilia and flagella.
Encyclopaedia of molecular cell biology and molecular medicine, 2nd edition, volume 8 (2005), WILEY-VCH Verlag GmbH & Co. KgaA, Weinheim.

Suzuki, H., Yonekura, K. and Namba, K.
Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis.
J. Mol. Biol. (2004) 337: 105-113.

Maki-Yonekura, S., Yonekura, K. and Namba, K.
Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum.
Proc. Natl. Acad. Sci. USA (2003) 100: 15528-15533.

Yonekura, K., Toyoshima, C., Maki-Yonekura, S. and Namba, K.
GUI programs for processing individual images in early stages of helical image reconstruction. --- for high-resolution structure analysis.
J. Struct. Biol. (2003) 144: 184-194.

Yonekura, K., Maki-Yonekura, S. and Namba, K.
Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy.
Nature (2003) 424: 623-650.

Yonekura, K., Maki-Yonekura, S. and Namba, K.
Growth mechanism of the bacterial flagellar filament.
Res. Microbiol. (2002) 153: 191-197.

Yonekura, K., Maki-Yonekura, S. and Namba, K.
Quantitative comparison of zero-loss and conventional electron diffraction from 2D and thin 3D protein crystals.
Biophys. J. (2002) 82:2784-2797.

Yonekura, K., Maki-Yonekura, S. and Namba, K.
Structure analysis of the flagellar cap-filament complex by electron cryomicroscopy and single-particle image analysis.
J. Struct. Biol. (2001) 133:246-253

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 (2000) 290:2148-2152.

Yonekura K. and Toyoshima C.
Structure determination of tubular crystals of membrane proteins. III. Solvent flattening.
Ultramicroscopy (2000) 84:29-45

Yonekura K. and Toyoshima C.
Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes.
Ultramicroscopy (2000) 84:15-28

Zhang, P., Toyoshima, C., Yonekura, K., Green, N. M. and Stokes, D.L.
Structure of the calcium pump from sarcoplasmic reticulum at 8-A resolution.
Nature (1998) 392:835-839

Yonekura, K., Stokes D. L., Sasabe, H. and Toyoshima, C.
The ATP-binding site of Ca2+-ATPase revealed by electron image analysis.
Biophys. J. (1997) 72:997-1005

Toyoshima, C., Yonekura, K. and Sasabe, H.
Contrast transfer for frozen-hydrated specimens II. Amplitude contrast at very low frequencies.
Ultramicroscopy (1993) 48:165-176.