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X-ray crystallography of molecular complexes regulating vesicular trafficking

Planned Research

Project AreaStructural basis of cell-signalling complexes mediating signal perception, transduction and responses
Project/Area Number 22121003
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

FUKAI Shuya  東京大学, 放射光連携研究機構, 准教授 (10361792)

Co-Investigator(Renkei-kenkyūsha) ATSUSHI Yamagata  東京大学, 放射光連携研究機構, 助教 (20463903)
SATO Yusuke  東京大学, 放射光連携研究機構, 助教 (50568061)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥220,740,000 (Direct Cost: ¥169,800,000、Indirect Cost: ¥50,940,000)
Fiscal Year 2014: ¥29,120,000 (Direct Cost: ¥22,400,000、Indirect Cost: ¥6,720,000)
Fiscal Year 2013: ¥30,550,000 (Direct Cost: ¥23,500,000、Indirect Cost: ¥7,050,000)
Fiscal Year 2012: ¥31,980,000 (Direct Cost: ¥24,600,000、Indirect Cost: ¥7,380,000)
Fiscal Year 2011: ¥31,720,000 (Direct Cost: ¥24,400,000、Indirect Cost: ¥7,320,000)
Fiscal Year 2010: ¥97,370,000 (Direct Cost: ¥74,900,000、Indirect Cost: ¥22,470,000)
Keywords分子認識 / シグナル伝達 / タンパク質複合体 / X線結晶構造解析 / 構造生物学 / 小胞輸送 / 低分子量GTPase
Outline of Final Research Achievements

Eukaryotic cells are composed of various organelles, which are compartmentalized by lipid bilayer. Therefore, transport between spatially separated organelles is mediated by membrane vesicles. Vesicular transports play critical roles in cellular processes including cell motility, deformation and polarization. In this research project, we revealed some of the regulatory mechanisms for vesicular transport at the atomic resolution level by X-ray crystallography of molecular complexes that are involved in vesicular transport. Moreover, technology platform that has been developed through this project was applied to collaborative researches to elucidate protein complex-mediated regulatory mechanisms for other cellular functions.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (25 results)

All 2015 2014 2013 2012 2011 2010

All Journal Article (13 results) (of which Peer Reviewed: 12 results,  Open Access: 5 results,  Acknowledgement Compliant: 4 results) Presentation (11 results) (of which Invited: 5 results) Book (1 results)

  • [Journal Article] Mechanisms of splicing-dependent trans-synaptic adhesion by PTPδ-IL1RAPL1/IL-1RAcP for synaptic differentiation2015

    • Author(s)
      Yamagata A., Yoshida, T., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Iwasawa-Okamoto, S., Mori, H., Mishina, M., Fukai , S.
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 6926-6926

    • DOI

      10.1038/ncomms7926

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structure of Slitrk2-PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion2015

    • Author(s)
      Yamagata A., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Yoshida, T., Fukai , S.
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 9686-9686

    • DOI

      10.1038/srep09686

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP202015

    • Author(s)
      Toma, A, Takahashi, T. S., Sato, Y., Yamagata, A., Goto-Ito, S., Nakada, S., Fukuto, A., Horikoshi, Y., Tashiro, S., Fukai, S.
    • Journal Title

      PLoS One

      Volume: 10 Issue: 3 Pages: 1-15

    • DOI

      10.1371/journal.pone.0120887

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity2015

    • Author(s)
      Sato, Y., Goto, E., Shibata, Y., Kubota, Y., Yamagata, A., Goto-Ito, S., Kubota, K., Inoue, J., Takekawa, M., Tokunaga, F. and Fukai, S.
    • Journal Title

      Nat. Struct. Mol. Biol.

      Volume: 22 Issue: 3 Pages: 222-229

    • DOI

      10.1038/nsmb.2970

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Switching and emergence of CTL epitopes in HIV-1 infection2014

    • Author(s)
      Han, C., Kawana-Tachikawa, A., Shimizu, A., Zhu D., Nakamura, H., Adachi, E., Kikuchi, T., Koga, M., Koibuchi, T., Gao, G.F., Sato, Y., Yamagata, A., Martin, E., Fukai, S., Brumme, Z.L.,Iwamoto, A.
    • Journal Title

      Retrovirolgy

      Volume: 11 Issue: 1 Pages: 38-38

    • DOI

      10.1186/1742-4690-11-38

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Core structures of ubiquitin dictate its dynamics and function2014

    • Author(s)
      Fukai, S.
    • Journal Title

      Journal of Molecular Biology

      Volume: 426 Issue: 7 Pages: 1367-1369

    • DOI

      10.1016/j.jmb.2013.12.008

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Switching and emergence of CTL epitopes in HIV-1 infection2014

    • Author(s)
      Han, C. Kawana-Tachikawa, A., Shimizu, A., Zhu, D., Nakamura, H., Adachi, E., Kikuchi, T., Koga, M., Koibuchi, T., Gao, G.G., Sato, Y., Yamagata, A., Martin, E., Fukai, S., Brumme, Z.L., Iwamoto, A.
    • Journal Title

      Retrovirology

      Volume: 未定

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection2013

    • Author(s)
      Shimizu, A., Kawana-Tachikawa. A., Yamagata, A., Han, C., Zhu, D., Sato, Y., Nakamura, H., Koibuchi, T., Carlson, J., Martin, E., Brumme, C.J., Shi, Y., Gao, G.F., Brumme, Z.L., Fukai, S., Iwamoto, A.
    • Journal Title

      Scientific Reports

      Volume: 3 Issue: 1 Pages: 3097-3097

    • DOI

      10.1038/srep03097

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces.2012

    • Author(s)
      Kubota K, Yamagata A, Sato Y, Goto-Ito S, Fukai S.
    • Journal Title

      J Mol Biol.

      Volume: 422(3) Issue: 3 Pages: 366-75

    • DOI

      10.1016/j.jmb.2012.05.045

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13.2012

    • Author(s)
      Sato Y, Yamagata A, Goto-Ito S, Kubota K, Miyamoto R, Nakada S, Fukai S.
    • Journal Title

      J Biol Chem.

      Volume: 287(31) Issue: 31 Pages: 25860-8

    • DOI

      10.1074/jbc.m112.364752

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ポリユビキチン鎖選択的結合による細胞機能制御2012

    • Author(s)
      佐藤裕介,深井周也
    • Journal Title

      生化学

      Volume: 84 Pages: 776-779

    • NAID

      10031122383

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Specific recognition of linear ubiquitin chains by the Npl4 zinc finger(NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex2011

    • Author(s)
      Sato, Y., Fujita, H., Yoshikawa, A., Yamashita, M., Yamagata, A., Kaiser, S. E., Iwai, K., Fukai, S
    • Journal Title

      Proceedings of National Academy of Science United States of America

      Volume: 108巻 Issue: 51 Pages: 20520-20525

    • DOI

      10.1073/pnas.1109088108

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] tructure and function of SecDF, a protein export-enhancing membrane component2011

    • Author(s)
      Tsukazaki, T., et al
    • Journal Title

      Nature

      Volume: 475 Issue: 7350 Pages: 235-238

    • DOI

      10.1038/nature09980

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] マルチサブユニット繋留因子複合体の全体構造決定へのアプローチ2014

    • Author(s)
      深井 周也
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ユビキチン鎖による炎症シグナル制御の構造基盤2014

    • Author(s)
      深井 周也
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      国立京都国際会館
    • Year and Date
      2014-10-15
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 中程度の分解能での結晶構造解析2014

    • Author(s)
      深井 周也
    • Organizer
      第14回日本蛋白質科学会年会
    • Place of Presentation
      ワークピア横浜
    • Year and Date
      2014-06-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Structural basis for selective cleavage of M1- and K63-linked polyubiquitin chains by a CYLD deubiquitinase2013

    • Author(s)
      Shuya Fukai, Yusuke Sato
    • Organizer
      Cold Spring Harbor Laboratory 2013 meeting - The Ubiquitin Family
    • Place of Presentation
      Cold Spring Harbor Laboratory, 米国
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Structural basis for recognition of ubiquitin by UMI domain of RNF1682013

    • Author(s)
      Yusuke Sato, Aya Toma, Shuya Fukai
    • Organizer
      Cold Spring Harbor Laboratory 2013 meeting - The Ubiquitin Family
    • Place of Presentation
      Cold Spring Harbor Laboratory, 米国
    • Related Report
      2013 Annual Research Report
  • [Presentation] Get3による翻訳後膜埋め込み機構の構造学的基盤2012

    • Author(s)
      山形敦史,窪田恵子,後藤(伊藤)桜子,佐藤裕介,深井周也
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2012-12-11
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 構造解析のためのユビキチン鎖の大量合成2011

    • Author(s)
      深井周也
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク(大阪府吹田市)(招待講演)
    • Year and Date
      2011-06-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Structural basis of ubiquitin chain recognition by NZF domains for NF-κB activation2011

    • Author(s)
      深井周也
    • Organizer
      TNF2011(第13回国際TNF会議)
    • Place of Presentation
      淡路夢舞台国際会議場(兵庫県淡路市)(招待講演)
    • Year and Date
      2011-05-18
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mechanisms for recognition of K63-linked polyubiquitin chains2010

    • Author(s)
      深井周也
    • Organizer
      Pacifichem2010
    • Place of Presentation
      大阪大学コンベンションセンター(吹田キャンパス)
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] 繋留複合体による膜融合制御の構造基盤2010

    • Author(s)
      深井周也
    • Organizer
      BMB2010
    • Place of Presentation
      神戸ポートピアランド
    • Year and Date
      2010-12-10
    • Related Report
      2010 Annual Research Report
  • [Presentation] Znフィンガーによるユビキチン鎖識別のメカニズム2010

    • Author(s)
      深井周也
    • Organizer
      平成22年度日本結晶学会年会
    • Place of Presentation
      大阪大学コンベンションセンター(吹田キャンパス)
    • Year and Date
      2010-12-05
    • Related Report
      2010 Annual Research Report
  • [Book] 細胞工学 29巻[特集]ユビキチン修飾系の多彩な機能2010

    • Author(s)
      深井周也
    • Publisher
      秀潤社
    • Related Report
      2010 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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