Centers & Labs

RIKEN SPring-8 Center

Bio-Specimen Platform Group

Group Director: Naoki Kunishima (D.Sci.)
Naoki  Kunishima(D.Sci.)

To understand rationally the function of protein that supports life activities, it is necessary to determine its 3D-structure at atomic level. The X-ray crystallography analysis had previously been the most efficient and popular way to determine protein 3D-structures at atomic level. However, it was revealed that proteins which can crystallize were only 40% of all genomes, even in the proteins originated in thermo-stable microorganism, as a result of structural genomics. It is too hard to crystallize the rest 60% proteins by conventional technology. To construct a high-throughput framework for the structure determination of challenging targets such as membrane proteins, we develop a new methodology using XFEL as well as extend the technical basis of protein crystallography established in the Protein 3000 Project.

Main Research Field


Related Research Fields

Complex systems / Medicine, dentistry, and pharmacy


  • Protein crystal engineering
  • Design of hyper-thermostable proteins
  • Structure-based drug design

Selected Publications

  1. Naitow H., Matsuura Y., Tono K., Joti Y., Kameshima T., Hatsui T., Yabashi M., Tanaka R., Tanaka T., Sugahara M., Kobayashi J., Nango E., Iwata S., and Kunishima N.:
    "Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation"
    Acta Crystallogr. D73, 702-709 (2017).
  2. Matsuura Y., Takehira M., Joti Y., Ogasahara K., Tanaka T., Ono N., Kunishima N., and Yutani K.:
    "Thermodynamics of protein denaturation at temperatures over 100 ℃: CutA1 mutant proteins substituted with hydrophobic and charged residues"
    Sci. Rep. 5, 15545 (2015).
  3. Satoh M., Saburi H., Tanaka T., Matsuura Y., Naitow H., Shimozono R., Yamamoto N., Inoue H., Nakamura N., Yoshizawa Y., Aoki T., Tanimura R., and Kunishima N.:
    "Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation"
    FEBS Open Bio 5, 557-570 (2015).
  4. Sugahara M., Mizohata E., Nango E., Suzuki M., Tanaka T., Masuda T., Tanaka R., Shimamura T., Tanaka Y., Suno C., Ihara K., Pan D., Kakinouchi K., Sugiyama S., Murata M., Inoue T., Tono K., Song C., Park J., Kameshima T., Hatsui T., Joti Y., Yabashi M., and Iwata S.:
    "Grease matrix as a versatile carrier of proteins for serial crystallography"
    Nature Methods 12, 61-63 (2015).
  5. Asada Y., Sugahara M., Mizutani H., Naitow H., Tanaka T., Matsuura Y., Agari Y., Ebihara A., Shinkai A., Kuramitsu S., Yokoyama S., Kaminuma E., Kobayashi N., Nishikata K., Shimoyama S., Toyoda T., Ishikawa T., and Kunishima N.:
    "Integrated database of information from structural genomics experiments"
    Acta Crystallogr. D69, 914-919 (2013).
  6. Matsuura Y, Takehira M, Sawano M, Ogasahara K, Tanaka T, Yamamoto H, Kunishima N, Kato E, and Yutani K.:
    "Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 ℃"
    FEBS J. 279, 78-90 (2012).
  7. Sugahara M., Kageyama-Morikawa Y., and Kunishima N.:
    "Packing space expansion of protein crystallization screening with synthetic zeolite as a heteroepitaxic nucleant"
    Crystal Growth & Design 11, 110-120 (2011).
  8. Mizutani, H., Saraboji, K., Malathy-Sony, S. M., Ponnuswamy, M. N., Kumarevel, T., Krishna-Swamy, B. S., Simanshu, D. K., Murthy, M. R. N., and Kunishima, N.:
    "Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality"
    Acta Crystallogr. D 64, 1020-1033 (2008).
  9. Sugahara, M., Asada, Y., Shimizu, K., Yamamoto, H., Lokanath, N. K., Mizutani, H., Bagautdinov, B., Matsuura, Y., Taketa, M., Kageyama, Y., Ono, N., Morikawa, Y., Tanaka, Y., Shimada, H., Nakamoto, T., Sugahara, Mitsu., Yamamoto, M., and Kunishima, N.:
    "High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center"
    J. Struct. Funct. Genomics 9, 21-28 (2008).
  10. Bagautdinov, B., Matsuura, Y., Bagautdinova, S., and Kunishima, N.:
    "Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate"
    J. Biol. Chem. 283, 14739-14750 (2008).

Lab Members

Principal Investigator

Naoki Kunishima
Group Director

Core Members

Hisashi Naito
Senior Research Scientist
Saori Maki
Research Scientist
Yoshinori Matsuura
Research Associate

Contact information

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

Email: kunisima [at]

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