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

• Project/Area Number: 26840023
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Okayama 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: ¥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.

Research Products

• [Journal Article] Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex (2016)
  • 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
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex (2015)
  • 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
  • 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 II (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Theoretical studies of the damage-free SI structure of the CaMn405 cluster in oxygen-evolving complex of photosystem II (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses (2015)
  • 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
  • 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
  • Invited
• [Presentation] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex (2016)
  • 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
  • Invited
• [Presentation] Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution revealed by XFEL pulses (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution revealed by XFEL pulses (2015)
  • Author(s): M. Suga
  • Organizer: Japan-Korea joint workshop on XFEL sciences
  • Place of Presentation: Gyeongju, Korea
  • Year and Date: 2015-10-22
  • 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
• [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
  • 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
  • Invited
• [Presentation] Radiation damage free structure of photosystem II at 1.95 Å resolution (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Radiation damage free structure of photosystem II in the S1 state at 1.95 Å resolution (2015)
  • 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
  • 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
  • Invited
• [Presentation] Radiation damage free structure of oxygen evolving photosystem II at 1.95Å resolution revealed by X-ray Free Electron Laser (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: 第6回日本光合成学会年会
  • Place of Presentation: 岡山県
  • Year and Date: 2015-05-22
• [Presentation] Radiation damage free structure of photosystem II at 1.95A resolution (2015)
  • Author(s): Michi Suga
  • Organizer: The 1st SACLA Workshop on Femtosecond Crystallography
  • Place of Presentation: 兵庫県
  • Year and Date: 2015-03-26
  • 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
  • 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
• [Presentation] Native structure of photosystem II at 1.95A resolution revealed by a femtosecond X-ray laser (2014)
  • Author(s): M. Suga et al
  • Organizer: ICARP 2014
  • Place of Presentation: 兵庫県
  • Year and Date: 2014-11-24
• [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
• [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
• [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
• [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
• [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
• [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