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Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å


Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 Å. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 Å. From our electron density map, we located all of the metal atoms of the Mn4CaO5 cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

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Figure 1: Overall structure of PSII dimer from T. vulcanus at a resolution of 1.9 Å.
Figure 2: Structure of the Mn 4 CaO 5 cluster.
Figure 3: Hydrogen-bond network around YZ.
Figure 4: Structure of two Cl -binding sites.
Figure 5: Organization of chlorophylls.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates have been deposited in the Protein Data Bank under the accession number 3ARC.


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The X-ray diffraction data was taken at beamlines BL44XU, BL41XU and BL38B1 at SPring-8. We thank E. Yamashita, N. Shimizu, S. Baba and N. Mizuno for their help in using the beamlines. J.-R.S. thanks Y. Inoue for his support in the initiation of this work. This work was supported by a Grant-in-Aid for Scientific Research on Priority Areas (Structures of Biological Macromolecular Assemblies), a Grant-in-Aid for Creative Scientific Research, a GCOE programme on Pico-biology at the University of Hyogo, a Grant-in-Aid for Scientific Research (C), from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and a research grant from the Yamada Science foundation.

Author information




K.K. performed, and J.-R.S. supervised, the purification and crystallization of PSII. K.K., Y.U. and J.-R.S. performed X-ray diffraction experiments. Y.U. analysed the structure, and N.K. supervised the structure analysis and refinement process. J.-R.S. and N.K. jointly wrote the paper, and all of the authors joined the discussion of the results.

Corresponding authors

Correspondence to Jian-Ren Shen or Nobuo Kamiya.

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The authors declare no competing financial interests.

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This file contains Supplementary Tables 1-5, Supplementary Figures 1-6 with legends, Supplementary Data and Results, and additional references. (PDF 1710 kb)

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Umena, Y., Kawakami, K., Shen, JR. et al. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 473, 55–60 (2011).

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