Letter | Published:

Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses

Nature volume 517, pages 99103 (01 January 2015) | Download Citation


Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment1. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation2, and slight differences were found in the Mn–Mn distances determined by XRD1, EXAFS3,4,5,6,7 and theoretical studies8,9,10,11,12,13,14. Here we report a ‘radiation-damage-free’ structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn–Mn distances that are shorter by 0.1–0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(iii), Mn2C(iv), Mn3B(iv) and Mn4A(iii), based on the average Mn–ligand distances and analysis of the Jahn–Teller axis on Mn(iii). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

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Coordinates and structure factors for the structure determination have been deposited in the Protein Data Bank with accession codes 4UB6 and 4UB8 for data sets 1 and 2, respectively.


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We thank T. Ishikawa, M. Yabashi, K. Tono and Y. Inubushi for help in using the SACLA beamline, T. Tsukihara and S. Yoshikawa for suggestions and comments on the experiments, F. Seno for assistance with sample preparation, and K. Kawakami and Y. Umena for suggestions in the initial stage of the project. F. H. M. Koua participated in the initial stage of this work. This work was supported by an X-ray Free Electron Laser Priority Strategy Program (The Ministry of Education, Culture, Sports, Science and Technology of Japan, MEXT) (H.A. and J.-R.S.), a JST/CREST grant (K.H.), a grant-in-aid for Specially Promoted Research no. 24000018 (J.-R.S.) and KAKENHI grant no. 26840023 (M.S.) from JSPS, MEXT, Japan. The XFEL experiments were performed at beamline 3 of SACLA with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (proposal nos 2012A8011, 2012B8040, 2013A8047, 2013B8052 and 2014A8036), and we thank staff at SACLA for their help.

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Author notes

    • Michihiro Suga
    •  & Fusamichi Akita

    These authors contributed equally to this work.


  1. Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan

    • Michihiro Suga
    • , Fusamichi Akita
    • , Yoshiki Nakajima
    • , Tetsuya Shimizu
    •  & Jian-Ren Shen
  2. RIKEN SPring-8 Center, 1-1-1 Kouto Sayo, Hyogo 679-5148, Japan

    • Kunio Hirata
    • , Go Ueno
    • , Hironori Murakami
    • , Keitaro Yamashita
    • , Masaki Yamamoto
    •  & Hideo Ago
  3. Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama 332-0012, Japan

    • Kunio Hirata


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H.A. and J.-R.S. planned and organized the experiments, F.A. and Y.N. prepared the samples, F.A. made the crystals, G.U., H.M., K.H., H.A. and M.Y. designed and established the experimental set-up, M.S., F.A., T.S., Y.N., G.U., H.M., K.H., H.A., M.Y. and J.-R.S. conducted the diffraction experiments, K.Y. performed scaling of raw diffraction images, M.S. performed the structural analysis, M.S. and J.-R.S. wrote the manuscript, and all authors discussed and commented on the results and the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Masaki Yamamoto or Hideo Ago or Jian-Ren Shen.

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