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Visualization of Coulomb potential by electron crystallography

Research Project

Project/Area Number 24657111
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

YONEKURA Koji  独立行政法人理化学研究所, 放射光科学総合研究センター, 准主任研究員 (50346144)

Co-Investigator(Kenkyū-buntansha) MAKI Saori (YONEKURA Saori)  独立行政法人理化学研究所, 放射光科学総合研究センター, 研究員 (20513386)
Co-Investigator(Renkei-kenkyūsha) TOYOSHIMA Chikashi  東京大学, 分子細胞生物学研究所, 教授 (70172210)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords構造生物学 / 結晶構造解析 / 電子顕微鏡 / 膜蛋白質 / 超分子複合体 / Ca2+-ATPase / カタラーゼ
Outline of Final Research Achievements

Electron crystallography has the potential to analyze crystals of membrane proteins and macromolecular complexes too small or too thin for X-ray crystallography, as electrons are scattered 4 - 5 orders of magnitude more strongly than X-rays. Electron crystallography yields Coulomb potential maps, rather than electron density maps as X-rays do, providing information on charged states of amino-acids and metals. We presented such Coulomb potential maps at 3.4 and 3.2 Angstrom resolution, respectively, of calcium-ATPase and catalase obtained from crystals of just a few layers thick. These maps demonstrate that it is indeed possible to build atomic models from such crystals and charge information is included, often critical in understanding protein function.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (34 results)

All 2015 2014 2013 2012 Other

All Journal Article (10 results) (of which Peer Reviewed: 6 results,  Open Access: 2 results) Presentation (20 results) (of which Invited: 8 results) Book (1 results) Remarks (3 results)

  • [Journal Article] Electron crystallography of ultrathin 3D protein crystals : Atomic models with charges2015

    • Author(s)
      K. Yonekura, K. Kato, M. Ogasawara, M. Tomita and C. Toyoshima
    • Journal Title

      Proc. Nat. Acad. Sci. USA

      Volume: 112 Issue: 11 Pages: 3368-3373

    • DOI

      10.1073/pnas.1500724112

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Signal-enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects2015

    • Author(s)
      Y. Takayama, S. Maki-Yonekura, T. Oroguchi, M. Nakasako and K. Yonekura
    • Journal Title

      Sci. Rep.

      Volume: 5 Issue: 1 Pages: 8074-8074

    • DOI

      10.1038/srep08074

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single shot three-dimensional imaging of high-index-faceted nanocrystals with femtosecond X-ray free electron laser pulses2014

    • Author(s)
      R. Xu, H. Jiang, C. Song, Z. Huang, J. A. Rodriguez, C-C. Chen, D. Nam, J. Park, M. Gallagher-Jones, S. Kim, S. Kim, A. Suzuki, Y. Takayama, T. Oroguchi, Y. Takahashi, J. Fan, Y. Zou, T. Hatsui, Y. Inubushi, T. Kameshima, K. Yonekura et al.
    • Journal Title

      Nat. Commun.

      Volume: 5 Issue: 1 Pages: 4061-4061

    • DOI

      10.1038/ncomms5061

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] X線自由電子レーザーを用いた非結晶粒子のコヒーレントX 線回折イメージング2014

    • Author(s)
      中迫雅由, 苙口友隆, 関口優希, 小林周, 橋本早紀, 白濱圭也, 山本雅貴, 高山裕貴, 米倉功治, 眞木さおり, 引間孝明, 高橋幸生, 鈴木明大, 松永幸大, 乾弥生, 登野健介, 亀島敬, 城地保昌, 犬伏雄一, 星貴彦
    • Journal Title

      日本結晶学会誌

      Volume: 56 Pages: 27-35

    • NAID

      130003395580

    • Related Report
      2013 Research-status Report
  • [Journal Article] Post-transcriptional regulator Hfq binds catalase HPII: crystal structure of the complex2013

    • Author(s)
      Yonekura, K., Watanabe, M., Kageyama, Y., Hirata, K., Yamamoto, M. and Maki-Yonekura, S.
    • Journal Title

      PLOS ONE (2013)

      Volume: 8 Issue: 11 Pages: e78216-e78216

    • DOI

      10.1371/journal.pone.0078216

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus2013

    • Author(s)
      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.
    • Journal Title

      Molecular Cell

      Volume: 52 Issue: 1 Pages: 135-145

    • DOI

      10.1016/j.molcel.2013.09.013

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging2013

    • Author(s)
      Masayoshi Nakasako, Yuki Takayama, Tomotaka Oroguchi, et al.
    • Journal Title

      Review of Scientific Instruments

      Volume: 84 Issue: 9 Pages: 93705-93705

    • DOI

      10.1063/1.4822123

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] 低温電子顕微鏡法による蛋白質構造の可視化2013

    • Author(s)
      米倉功治, 眞木さおり
    • Journal Title

      感染 炎症 免疫

      Volume: 43 Pages: 307-312

    • Related Report
      2013 Research-status Report
  • [Journal Article] 非結晶粒子のコヒーレントX線回折イメージング2012

    • Author(s)
      中迫雅由、高山裕貴、苙口友隆、白濱圭也、関口優希、山本雅貴、米倉功治、引間孝明、眞木さおり、高橋幸生、鈴木明大、松永幸大、加藤翔一、星貴彦
    • Journal Title

      レーザー研究

      Volume: 40 Pages: 680-686

    • NAID

      10031004094

    • Related Report
      2012 Research-status Report
  • [Journal Article] X線自由電子レーザーを用いた非結晶粒子のコヒーレントX線回折イメージング実験2012

    • Author(s)
      中迫雅由、高山裕貴、苙口友隆、白濱圭也、関口優希、山本雅貴、米倉功治、引間孝明、眞木さおり、高橋幸生、鈴木明大、松永幸大、加藤翔一、星貴彦
    • Journal Title

      月刊OPTRONICS

      Volume: 31 Pages: 101-106

    • Related Report
      2012 Research-status Report
  • [Presentation] 低温電子顕微鏡における三次元再構成2015

    • Author(s)
      米倉功治
    • Organizer
      SACLAにおける低温X線回折イメージング実験の展開と標準化
    • Place of Presentation
      慶応大学 矢上キャンパス
    • Year and Date
      2015-03-20
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 低温電子顕微鏡法による三次元結晶と単粒子構造解析2015

    • Author(s)
      米倉功治
    • Organizer
      平成26年度「分子システム研究」研究報告会
    • Place of Presentation
      埼玉 和光
    • Year and Date
      2015-02-24 – 2015-02-25
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 低温電子顕微鏡法によるタンパク質構造解析 “膜タンパク質及びタンパク質複合体への応用”2014

    • Author(s)
      米倉功治
    • Organizer
      理研-武田WS「インシリコ技術による効率的な創薬手法の開発」 ~ タンパク質構造解析の最前線 ~
    • Place of Presentation
      武田薬品工業(株) 湘南研究所
    • Year and Date
      2014-10-28
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Electron Crystallography of Thin Protein Crystals2014

    • Author(s)
      Koji Yonekura
    • Organizer
      第87回日本生化学会大会 「生化学研究における電子顕微鏡技術の最前線」 The cutting edge of electron microscopy for the field of biochemistry
    • Place of Presentation
      京都府 京都国際会館
    • Year and Date
      2014-10-16
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Electron Crystallography of 3D Protein Crystals2014

    • Author(s)
      Koji Yonekura
    • Organizer
      Gordon Research Conference: Three Dimensional Electron Microscopy
    • Place of Presentation
      Girona, Spain
    • Year and Date
      2014-06-22 – 2014-06-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Electron Crystallography of an Energizing Channel Complex2014

    • Author(s)
      Saori Maki-Yonekura
    • Organizer
      Gordon Research Conference: Three Dimensional Electron Microscopy
    • Place of Presentation
      Girona, Spain
    • Year and Date
      2014-06-22 – 2014-06-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 蛋白質の薄い三次元結晶の電子線結晶構造解析2014

    • Author(s)
      米倉功治
    • Organizer
      平成25年度「分子システム研究」研究報告会
    • Place of Presentation
      理化学研究所 (埼玉県)
    • Related Report
      2013 Research-status Report
  • [Presentation] 電子顕微鏡による三次元再構成2014

    • Author(s)
      米倉功治
    • Organizer
      X線自由電子レーザー重点課題 「SACLAにおける低温X線回折イメージング実験の展開と標準化」 コヒーレントX線回折イメージングにおけるデータ収集と構造解析の現状と将来
    • Place of Presentation
      慶應義塾大学 (神奈川県)
    • Related Report
      2013 Research-status Report
  • [Presentation] SPring-8 - 医療分野での展望 -2013

    • Author(s)
      米倉功治
    • Organizer
      兵庫県保険医協会姫路・西播支部第28回支部総会・記念講演会, 姫路, 7月 (2013)
    • Place of Presentation
      西はりま地場産業センター (兵庫県)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] SACLAにおける低温X線回折イメージング- べん毛、大腸菌等 -2013

    • Author(s)
      米倉功治, 眞木さおり, 高山裕貴
    • Organizer
      X線自由電子レーザー重点課題 「SACLAにおける低温X線回折イメージング実験の展開と標準化」 第二回会合
    • Place of Presentation
      理化学研究所 (埼玉県)
    • Related Report
      2013 Research-status Report
  • [Presentation] Cryo-Electron Microscopy of Biological Macromolecular Structures2013

    • Author(s)
      K. Yonekura, S. Maki-Yonekura
    • Organizer
      4-th France-Japan Joint Seminar "Imaging of spatiotemporal hierarchies in living cells - an overview of dynamics from molecules to cells -"
    • Place of Presentation
      RIKEN SPring-8 Center (Hyogo)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Structure Analysis of Biological Macromolecular Complexes by Electron- and X-rays2013

    • Author(s)
      K. Yonekura
    • Organizer
      The 5th Biennale RIKEN Joint Retreat “Behavior - from Molecules, Cell to Organisms -"
    • Place of Presentation
      YAMAHA Resort Tsumagoi (Shizuoka)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Electron Crystallography of 3D Protein Crystals2013

    • Author(s)
      K. Yonekura, C. Toyoshima
    • Organizer
      Nagoya Symposium - Frontiers in Structural Physiology
    • Place of Presentation
      Nagoya University (Nagoya)
    • Related Report
      2012 Research-status Report
  • [Presentation] 電子線とX線による生体超分子構造の解析2013

    • Author(s)
      米倉功治
    • Organizer
      平成24年度「分子システム研究」成果報告会
    • Place of Presentation
      理研和光(埼玉)
    • Related Report
      2012 Research-status Report
  • [Presentation] 低温電子顕微鏡法による生体超分子複合体の構造解析2012

    • Author(s)
      米倉功治、眞木さおり
    • Organizer
      第13回医学生物学電子顕微鏡学会
    • Place of Presentation
      チサンホテル新大阪(大阪)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 細菌のイオン共役型エネルギー供与体の構造基盤研究2012

    • Author(s)
      渡邊真宏
    • Organizer
      分子システム研究」第1回春合宿
    • Place of Presentation
      浜名湖ロイヤルホテル(静岡)
    • Related Report
      2012 Research-status Report
  • [Presentation] 生体の作動機構をより高い分解能で“見る”2012

    • Author(s)
      米倉功治
    • Organizer
      分子システム研究」第1回春合宿
    • Place of Presentation
      浜名湖ロイヤルホテル(静岡)
    • Related Report
      2012 Research-status Report
  • [Presentation] イオン共役型エネルギー供与体ExbB/ExbDおよびTonB/ExbB複合体の結晶化構造解析2012

    • Author(s)
      渡邊真宏、米倉功治
    • Organizer
      第12回蛋白質科学会
    • Place of Presentation
      名古屋国際会議場(名古屋)
    • Related Report
      2012 Research-status Report
  • [Presentation] Purification and crystallization of bacterial ion-coupled energizing protein ExbB2012

    • Author(s)
      M. Watanabe, K. Yonekura
    • Organizer
      The 2012 Annual Meeting of American Crystallographic Association
    • Place of Presentation
      Boston(MA), USA
    • Related Report
      2012 Research-status Report
  • [Presentation] 細菌のイオン共役型エネルギー供与体の構造基盤研究2012

    • Author(s)
      渡邊真宏、米倉功治
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡(福岡)
    • Related Report
      2012 Research-status Report
  • [Book] SPring-8 - 医療分野での展望 -2013

    • Author(s)
      米倉 功治
    • Total Pages
      1
    • Publisher
      兵庫保険医新聞
    • Related Report
      2013 Research-status Report
  • [Remarks] 微小で薄いタンパク質結晶の電子線構造解析 -これまで利用できなかった結晶から電荷を可視化-

    • URL

      http://www.riken.jp/pr/press/2015/20150223_1/

    • Related Report
      2014 Annual Research Report
  • [Remarks] 理化学研究所ホームページ

    • URL

      http://www.riken.jp/pr/press/2013/20131107_1/

    • Related Report
      2013 Research-status Report
  • [Remarks] 米倉生体機構研究室

    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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