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Radiation damage free structure of photosystem II revealed by X-ray free electron laser.

Research Project

Project/Area Number 26840023
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Structural biochemistry
Research InstitutionOkayama University

Principal Investigator

Suga Michi  岡山大学, 自然科学研究科, 助教 (60634920)

Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Keywords光化学系II / 膜タンパク質 / 光合成 / 結晶構造解析 / X線自由電子レーザー / 無損傷 / 光化学系II複合体 / XFEL
Outline of Final Research Achievements

The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700 kDa membrane protein complex that catalyzes water-splitting reaction through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by XRD at 1.9 A resolution, which revealed that the OEC is a Mn4CaO5 cluster. However, the manganese atoms in the OEC are easily reduced by X-ray irradiation.
Recently, it was demonstrated that radiation damage free structure can be obtainable using X-ray free electron lasers (XFEL). We determined a radiation damage free structure of PSII in the S1 state at a resolution of 1.95 A using XFEL pulses. Compared with the structure from XRD, the OEC in the XFEL structure has Mn-Mn distances that are shorter by 0.1-0.2A. Based on the XFEL structure, the valences of each manganese atom were assigned as Mn1(+3), Mn2(+4), Mn3(+4) and Mn4(+3) in the S1 state. These findings provide a structural basis for the mechanism of oxygen evolution.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • Research Products

    (27 results)

All 2016 2015 2014 Other

All Journal Article (5 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 5 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (18 results) (of which Int'l Joint Research: 5 results,  Invited: 11 results) Remarks (4 results)

  • [Journal Article] Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex2016

    • Author(s)
      M. Suga, X. Qin, T. Kuang and J.R. Shen
    • Journal Title

      Current Opinion in Structural biology

      Volume: in press Pages: 46-53

    • DOI

      10.1016/j.sbi.2016.04.004

    • NAID

      120006337928

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex2015

    • Author(s)
      X. Qin, M. Suga, T. Kuang and J.R. Shen
    • Journal Title

      Science

      Volume: 348 Issue: 6238 Pages: 989-995

    • DOI

      10.1126/science.aab0214

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] On the guiding principles for lucid understanding of the damage-free Sl Structure of the CaMn405 cluster in the oxygen evolving complex of photosystem II2015

    • Author(s)
      M. Shoji, H. Isobe, S. Yamanaka, M. Suga, F. Akita, J.-R. Shen, K. Yamaguchi
    • Journal Title

      Chemical Physics Letters

      Volume: 627 Pages: 44-52

    • DOI

      10.1016/j.cplett.2015.03.033

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical studies of the damage-free SI structure of the CaMn405 cluster in oxygen-evolving complex of photosystem II2015

    • Author(s)
      M. Shoji, H. Isobe, S. Yamanaka, M. Suga, F. Akita, J.-R. Shen, K. Yamaguchi
    • Journal Title

      Chemical Physics Letters

      Volume: 623 Pages: 1-7

    • DOI

      10.1016/j.cplett.2015.01.030

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses2015

    • Author(s)
      Michihiro Suga, Fusamichi Akita, Kunio Hirata, Go Ueno, Hironori Murakami, Yoshiki Nakajima, Tetsuya Shimizu, Keitaro Yamashita, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen
    • Journal Title

      Nature

      Volume: 517 Issue: 7532 Pages: 99-103

    • DOI

      10.1038/nature13991

    • NAID

      120005656446

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Presentation] X線結晶構造解析による光化学系の 構造機能研究のこれまでとこれから2016

    • Author(s)
      菅倫寛
    • Organizer
      大阪大学蛋白質研究所セミナー 構造を基盤とする蛋白質科学における未解決問題
    • Place of Presentation
      東京
    • Year and Date
      2016-03-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex2016

    • Author(s)
      M. Suga
    • Organizer
      Bridging the gap: from structure to fuctional dynamics of photosynthesis related protein complexes
    • Place of Presentation
      大阪
    • Year and Date
      2016-02-02
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex2015

    • Author(s)
      Suga M, Qin X, Kuang T and Shen JR
    • Organizer
      The 13th Conference of the Asican Crystallographic Association (AsCA2015)
    • Place of Presentation
      Kolkata, India
    • Year and Date
      2015-12-05
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution revealed by XFEL pulses2015

    • Author(s)
      M. Suga
    • Organizer
      The 13th Conference of the Asican Crystallographic Association (AsCA2015)
    • Place of Presentation
      Kolkata, India
    • Year and Date
      2015-12-05
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution revealed by XFEL pulses2015

    • Author(s)
      M. Suga
    • Organizer
      Japan-Korea joint workshop on XFEL sciences
    • Place of Presentation
      Gyeongju, Korea
    • Year and Date
      2015-10-22
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 高等植物光化学系I-集捕集アンテナI 超複合体におけるエネルギー伝達経路の構造基盤2015

    • Author(s)
      菅倫寛,Xiaochun Qin, Tingyun Kuang,沈建仁
    • Organizer
      日本結晶学会2015年度年会
    • Place of Presentation
      大阪府
    • Year and Date
      2015-10-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] 酸素発生型光合成を司る光化学系II複合体と光化学系I複合体の結晶学的研究2015

    • Author(s)
      菅倫寛
    • Organizer
      日本結晶学会進歩賞受賞講演
    • Place of Presentation
      大阪府
    • Year and Date
      2015-10-17
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] X線自由電子レーザーによって明らかにされた光化学系II複合体の1.95Å分解能での無損傷構造2015

    • Author(s)
      菅倫寛,秋田総理,平田邦生,上野剛,村上博則,中島芳樹,清水哲哉,山下恵太郎,山本雅貴,吾郷日出夫,沈建仁
    • Organizer
      日本生物物理学会若手招待講演
    • Place of Presentation
      石川県
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution2015

    • Author(s)
      M. Suga, F. Akita, K. Hirata, G. Ueno, H. Murakami, Y. Nakajima, T. Shimizu, K.Yamashita, M. Yamamoto, H. Ago and J.-R. Shen
    • Organizer
      37th International Free Electron Laser Conference (FEL2015)
    • Place of Presentation
      Daejeon, Korea
    • Year and Date
      2015-08-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Radiation damage free structure of photosystem II in the S1 state at 1.95 Å resolution2015

    • Author(s)
      M. Suga, F. Akita, K. Hirata, G. Ueno, H. Murakami, Y. Nakajima, T. Shimizu, K.Yamashita, M. Yamamoto, H. Ago and J.-R. Shen
    • Organizer
      Gordon Research Conference on Photosynthesis
    • Place of Presentation
      Boston, USA
    • Year and Date
      2015-07-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] フェムト秒X線レーザーを用いた光化学系II複合体の1.95Å分解能での無損傷結晶構造解析2015

    • Author(s)
      菅倫寛,秋田総理,平田邦生,上野剛,村上博則,中島芳樹,清水哲哉,山下恵太郎,山本雅貴,吾郷日出夫,沈建仁
    • Organizer
      日本蛋白質科学会若手奨励賞シンポジウム
    • Place of Presentation
      徳島県
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Radiation damage free structure of oxygen evolving photosystem II at 1.95Å resolution revealed by X-ray Free Electron Laser2015

    • Author(s)
      菅倫寛,秋田総理,平田邦生,上野剛,村上博則,中島芳樹,清水哲哉,山下恵太郎,山本雅貴,吾郷日出夫,沈建仁
    • Organizer
      第6回日本光合成学会年会
    • Place of Presentation
      岡山県
    • Year and Date
      2015-05-22
    • Related Report
      2015 Annual Research Report
  • [Presentation] Radiation damage free structure of photosystem II at 1.95A resolution2015

    • Author(s)
      Michi Suga
    • Organizer
      The 1st SACLA Workshop on Femtosecond Crystallography
    • Place of Presentation
      兵庫県
    • Year and Date
      2015-03-26
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 光合成で酸素が発生する仕組み2015

    • Author(s)
      菅倫寛
    • Organizer
      テニュアトラック推進機構医学系物質科学分野セミナー「蛋白質立体構造解析の最前線」
    • Place of Presentation
      宮崎県
    • Year and Date
      2015-03-23
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] フェムト秒X 線自由電子レーザーによって得られた1.95A 分解能での天然状態の光化学系II 複合体の結晶構造2015

    • Author(s)
      菅倫寛ら
    • Organizer
      日本植物生理学会
    • Place of Presentation
      東京都
    • Year and Date
      2015-03-16
    • Related Report
      2014 Research-status Report
  • [Presentation] Native structure of photosystem II at 1.95A resolution revealed by a femtosecond X-ray laser2014

    • Author(s)
      M. Suga et al
    • Organizer
      ICARP 2014
    • Place of Presentation
      兵庫県
    • Year and Date
      2014-11-24
    • Related Report
      2014 Research-status Report
  • [Presentation] XFEL を用いた光化学系II 複合体の無損傷結晶構造解析2014

    • Author(s)
      菅倫寛ら
    • Organizer
      日本結晶学会年会
    • Place of Presentation
      東京都
    • Year and Date
      2014-11-01
    • Related Report
      2014 Research-status Report
  • [Presentation] Crystal structure at 1.5A resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongates.2014

    • Author(s)
      M. Suga et al
    • Organizer
      第5回日本光合成学会年会
    • Place of Presentation
      奈良県
    • Year and Date
      2014-05-30
    • Related Report
      2014 Research-status Report
  • [Remarks] 光合成光化学系I複合体の構造を解明~光エネルギーの高効率利用に前進~

    • URL

      http://www.okayama-u.ac.jp/tp/release/release_id303.html

    • Related Report
      2015 Annual Research Report
  • [Remarks] 高等植物の光化学系I-光捕集アンテナI超複合体におけるエネルギー伝達経路の構造基盤

    • URL

      http://first.lifesciencedb.jp/archives/10310

    • Related Report
      2015 Annual Research Report
  • [Remarks] フェムト秒X線レーザーにより明らかにされた1.95Å分解能における光化学系II複合体の天然状態の構造

    • URL

      http://first.lifesciencedb.jp/archives/9574

    • Related Report
      2015 Annual Research Report
  • [Remarks] 光化学系Ⅱ複合体の正確な三次元原子構造を解明 -人工光合成開発への糸口に-

    • URL

      http://www.okayama-u.ac.jp/tp/release/release_id251.html

    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2017-05-10  

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