Young, I.; Ibrahim, M.; Chatterjee, R.; Gul, S.; Fuller, F.; Koroidov, S.; Brewster, A.; Tran, R.; Alonso-Mori, R.; Kroll, T.; Michels-Clark, T.; Laksmono, H.; Sierra, R.; Stan, C.; Hussein, R.; Zhang, M.; Douthit, L.; Kubin, M.; De Lichtenberg, C.; Vo Pham, L.; Nilsson, H.; Cheah, M.; Shevela, D.; Saracini, C.; Bean, M.; Seuffert, I.; Sokaras, D.; Weng, T.; Pastor, E.; Weninger, C.; Fransson, T.; Lassalle, L.; Bräuer, P.; Aller, P.; Docker, P.; Andi, B.; Orville, A.; Glownia, J.; Nelson, S.; Sikorski, M.; Zhu, D.; Hunter, M.; Lane, T.; Aquila, A.; Koglin, J.; Robinson, J.; Liang, M.; Boutet, S.; Lyubimov, A.; Uervirojnangkoorn, M.; Moriarty, N.; Liebschner, D.; Afonine, P.; Waterman, D.; Evans, G.; Wernet, P.; Dobbek, H.; Weis, W.; Brunger, A.; Zwart, P.; Adams, P.; Zouni, A.; Messinger, J.; Bergmann, U.; Sauter, N.; Kern, J.; Yachandra, V.; Yano, J.: Structure of photosystem II and substrate binding at room temperature. Nature 540 (2016), p. 453-457
10.1038/nature20161

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 Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2,3. 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 site4–6. 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 (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8,9, 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 Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10–13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.