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High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center

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Journal of Structural and Functional Genomics

Abstract

A high-throughput crystallization-to-structure pipeline for structural genomics was recently developed at the Advanced Protein Crystallography Research Group of the RIKEN SPring-8 Center in Japan. The structure determination pipeline includes three newly developed technologies for automating X-ray protein crystallography: the automated crystallization and observation robot system “TERA”, the SPring-8 Precise Automatic Cryosample Exchanger “SPACE” for automated data collection, and the Package of Expert Researcher’s Operation Network “PERON” for automated crystallographic computation from phasing to model checking. During the 5 years following April, 2002, this pipeline was used by seven researchers to determine 138 independent crystal structures (resulting from 437 purified proteins, 234 cryoloop-mountable crystals, and 175 diffraction data sets). The protocols used in the high-throughput pipeline are described in this paper.

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Abbreviations

3-D:

Three-dimensional

APCR-group:

Advanced Protein Crystallography Research Group

MR:

Molecular replacement

PDB:

Protein Data Bank

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Acknowledgments

Of the authors, Michi. S. contributed principally to this work, solving structures and writing the paper; YA solved structures and contributed to the automated structure determination using PERON; KS solved structures and contributed to the automated diffraction experiment using SPACE; HY solved structures and contributed to large-scale protein production; NKL, HM, and BB solved structures; YM, MT, YK, NO, YM, YT, HS, and TN contributed to the construction of the structure determination pipeline; Mitsu. S. contributed to automated crystallization using TERA; MY contributed to the automated diffraction experiment using SPACE; NK supervised this work and wrote the paper. The authors would like to thank the staff of the RIKEN Genomic Science Center and the Structurome Research Group for providing plasmids, the technical staff of the RIKEN SPring-8 Center for assistance in the large-scale protein production, the beamline staff for assistance during the data collection at the BL26B1/B2 of SPring-8, and Drs M. Miyano, T. Iizuka, S. Yokoyama, and T. Ishikawa for their direction of the APCR-group. This work was supported by the “National Project on Protein Structural and Functional Analyses” funded by the Ministry of Education, Sports, Science, and Technology of Japan.

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Author notes

  1. Naoki Kunishima

    Present address: Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan

Authors and Affiliations

  1. Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan

    Michihiro Sugahara, Yukuhiko Asada, Katsumi Shimizu, Hitoshi Yamamoto, Neratur K. Lokanath, Hisashi Mizutani, Bagautdin Bagautdinov, Yoshinori Matsuura, Midori Taketa, Yuichi Kageyama, Naoko Ono, Yuko Morikawa, Yukiko Tanaka, Hiroki Shimada & Takanobu Nakamoto

  2. Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan

    Mitsuaki Sugahara

  3. Division of Synchrotron Radiation Instrumentation, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan

    Masaki Yamamoto

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  1. Michihiro Sugahara
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Correspondence to Naoki Kunishima.

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Sugahara, M., Asada, Y., Shimizu, K. et al. High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. J Struct Funct Genomics 9, 21–28 (2008). https://doi.org/10.1007/s10969-008-9042-y

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  • DOI: https://doi.org/10.1007/s10969-008-9042-y

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