5KAF

RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution

Summary for 5KAF

• Entry DOI: 10.2210/pdb5kaf/pdb
• Related: 5AKI 5TIS
• Descriptor: Photosystem II protein D1 1, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (36 entities in total)
• Functional Keywords: photosystems, transmembrane, room temperature, electron transport
• Biological source: Thermosynechococcus elongatus (strain BP-1); More
• Total number of polymer chains: 40
• Total formula weight: 761070.19

Authors

Young, I.D.,Ibrahim, M.,Chatterjee, R.,Gul, S.,Koroidov, S.,Brewster, A.S.,Tran, R.,Alonso-Mori, R.,Fuller, F.,Kroll, T.,Michels-Clark, T.,Laksmono, H.,Sierra, R.G.,Stan, C.A.,Saracini, C.,Bean, M.A.,Seuffert, I.,Sokaras, D.,Weng, T.-C.,Hunter, M.S.,Aquila, A.,Koglin, J.E.,Robinson, J.,Liang, M.,Boutet, S.,Lyubimov, A.Y.,Uervirojnangkoorn, M.,Moriarty, N.W.,Liebschner, D.,Afonine, P.V.,Waterman, D.G.,Evans, G.,Dobbek, H.,Weis, W.I.,Brunger, A.T.,Zwart, P.H.,Adams, P.D.,Zouni, A.,Messinger, J.,Bergmann, U.,Sauter, N.K.,Kern, J.,Yachandra, V.K.,Yano, J. (deposition date: 2016-06-01, release date: 2016-11-23, Last modification date: 2024-11-06)

Primary citation

Young, I.D.,Ibrahim, M.,Chatterjee, R.,Gul, S.,Fuller, F.D.,Koroidov, S.,Brewster, A.S.,Tran, R.,Alonso-Mori, R.,Kroll, T.,Michels-Clark, T.,Laksmono, H.,Sierra, R.G.,Stan, C.A.,Hussein, R.,Zhang, M.,Douthit, L.,Kubin, M.,de Lichtenberg, C.,Vo Pham, L.,Nilsson, H.,Cheah, M.H.,Shevela, D.,Saracini, C.,Bean, M.A.,Seuffert, I.,Sokaras, D.,Weng, T.C.,Pastor, E.,Weninger, C.,Fransson, T.,Lassalle, L.,Brauer, P.,Aller, P.,Docker, P.T.,Andi, B.,Orville, A.M.,Glownia, J.M.,Nelson, S.,Sikorski, M.,Zhu, D.,Hunter, M.S.,Lane, T.J.,Aquila, A.,Koglin, J.E.,Robinson, J.,Liang, M.,Boutet, S.,Lyubimov, A.Y.,Uervirojnangkoorn, M.,Moriarty, N.W.,Liebschner, D.,Afonine, P.V.,Waterman, D.G.,Evans, G.,Wernet, P.,Dobbek, H.,Weis, W.I.,Brunger, A.T.,Zwart, P.H.,Adams, P.D.,Zouni, A.,Messinger, J.,Bergmann, U.,Sauter, N.K.,Kern, J.,Yachandra, V.K.,Yano, J.
Structure of photosystem II and substrate binding at room temperature.
Nature, 540:453-457, 2016

PubMed Abstract: Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the MnCaO cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S to S), in which S is the dark-stable state and S is the last semi-stable state before O-O bond formation and O evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S), two-flash illuminated (2F; S-enriched), and ammonia-bound two-flash illuminated (2F-NH; S-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the MnCaO cluster in the S and S states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

PubMed: 27871088
DOI: 10.1038/nature20161

Experimental method

X-RAY DIFFRACTION (3.00000997771 Å)