Centers & Labs

Distinguished Senior Scientist Laboratories

Structural Biology Laboratory

Distinguished Senior Scientist: Shigeyuki Yokoyama (Ph.D.)
Shigeyuki  Yokoyama(Ph.D.)

We investigate the mechanisms underlying the extremely high specificities of the replication, transcription, and translation processes of the central dogma of molecular biology, "DNA makes RNA makes protein", with regard to the four bases and the twenty amino acids common to all organisms, at the level of the three-dimensional structures of protein•nucleic acid complexes by X-ray crystallographic structural studies. Furthermore, on the basis of the three-dimensional structures, we construct central dogma systems expanded with unnatural bases and amino acids. This combination of analytical and synthetic approaches allows us not only to understand the physicochemical mechanisms of the natural central dogma, but also to develop new biotechnologies with the advantages of the unnatural bases and amino acids. By using the expanded central dogma systems, we investigate the structures and functions of protein・nucleic acid complexes and membrane protein complexes, and develop targeted biologics.

Main Research Field

Biological Sciences

Related Research Fields

Chemistry / Biology / Medicine, dentistry, and pharmacy

Research Subjects

  • Structural biology of protein・nucleic acid complexes in replication, transcription, and translation
  • Synthetic biology of central dogma systems with unnatural bases and amino acids
  • Structural and synthetic biology of membrane protein complexes

Selected Publications

  1. Kazuhiro Kashiwagi, Mari Takahashi, Madoka Nishimoto, Takuya B. Hiyama, Toshiaki Higo, Takashi Umehara, Kensaku Sakamoto, Takuhiro Ito and Shigeyuki Yokoyama.:
    "Crystal structure of eukaryotic translation initiation factor 2B"
    Nature, 531 (7592), 122-125 (2016).
  2. Hiroaki Tanabe, Yoshifumi Fujii, Miki Okada-Iwabu, Masato Iwabu, Yoshihiro Nakamura, Toshiaki Hosaka, Kanna Motoyama, Mariko Ikeda, Motoaki Wakiyama, Takaho Terada, Noboru Ohsawa, Masakatsu Hato, Satoshi Ogasawara, Tomoya Hino, Takeshi Murata, So Iwata, Kunio Hirata, Yoshiaki Kawano, Masaki Yamamoto, Tomomi Kimura-Someya, Mikako Shirouzu, Toshimasa Yamauchi, Takashi Kadowaki and Shigeyuki Yokoyama.:
    "Crystal structures of the human adiponectin receptors"
    Nature, 520 (7547), 312-316 (2015).
  3. Naganuma, M., Sekine, S., Chong, Y. E., Guo, M., Yang, X. L., Gamper, H., Hou, Y. M., Schimmel, P., and Yokoyama, S.:
    "The selective tRNA aminoacylation mechanism based on a single G・U pair."
    Nature, 510, 507-511 (2014).
  4. Itoh, Y., Bröcker, M. J., Sekine, S., Hammond, G., Suetsugu, S., Söll, D. and and Yokoyama, S.:
    "Decameric SelA ・ tRNASec ring structure reveals mechanism of bacterial selenocysteine formation"
    Science, 340, 75-78 (2013).
  5. Tagami, S., Sekine, S., Kumarevel, T., Hino, N., Murayama, Y., Kamegamori, S., Yamamoto, M., Sakamoto, K. and Yokoyama, S.:
    "Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein"
    Nature, 468, 978-982 (2010).
  6. Ito, T. and Yokoyama, S.:
    "Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions"
    Nature, 467, 612-616 (2010).
  7. Shimada, A., Niwa, H., Tsujita, K., Suetsugu, S., Nitta, K., Hanawa-Suetsugu, K., Akasaka, R., Nishino, Y., Toyama, M., Chen, L., Liu, ZJ., Wang, BC., Yamamoto, M., Terada, T., Miyazawa, A., Tanaka, A., Sugano, S., Shirouzu, M., Nagayama, K., Takenawa, T. and Yokoyama, S.:
    "Curved EFC/F-BAR domain dimers are joined end to end into a filament for membrane invagination in endocytosis"
    Cell, 129, 761-772 (2007).
  8. Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S. and Yokoyama, S.:
    "Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa"
    Cell, 125, 287-300 (2006).
  9. Ishitani, R., Nureki, O., Nameki, N., Okada, N., Nishimura, S. and Yokoyama, S.:
    "Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme"
    Cell, 113, 383-394 (2003).
  10. Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, JH., Saito, K., Sakamoto, A., Inoue, M., Shirouzu, M. and Yokoyama, S.:
    "Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains"
    Cell, 110, 775-787 (2002).

Lab Members

Principal Investigator

Shigeyuki Yokoyama
Distinguished Senior Scientist

Core Members

Akeo Shinkai
Senior Research Scientist
Kumarevel Thirumananseri
Senior Research Scientist
Tetsuya Hori
Senior Research Scientist
Mitsuo Kuratani
Research Scientist
Eiko Seki
Research Scientist
Toru Sengoku
Research Scientist
Takaho Terada
Research Scientist
Yoshihiro Nakamura
Research Scientist
Wataru Nishii
Research Scientist
Yoshifumi Fujii
Research Scientist
Tomonari Muramatsu
Research Scientist
Tatsuo Yanagisawa
Research Scientist
Hiroyuki Kato
Technical Scientist
Masahito Kawazoe
Technical Scientist
Shingo Saito
Technical Scientist
Tomoko Nakayama
Technical Scientist
Kazuko Maekawa
Technical Scientist
Yasushi Hikida
Postdoctoral Researcher
Seisuke Kusano
Special technical staff
Hiroaki Tanabe
Special technical staff
Ayako Nomura
Special technical staff
Takako Imada
Part-time Worker

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: yokoyama [at] riken.jp

Related links

Recent research results

March 10, 2017: RIKEN RESEARCH
Switching sites for robust reproduction
April 9, 2015: Press Release
Obesity-related receptors have a unique structure