title: Structure of photosystem II and substrate binding at room temperature.
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 Mn4CaO5cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0to S4), in which S1is the dark-stable state and S3is the last semi-stable state before O-O bond formation and O2evolution. 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 (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 XFEL provided a damage-free view of the S1state, 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 Mn4CaO5cluster in the S2and S3states. 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.
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Iris D
authors.initials: ID
authors.lastname: Young
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Ibrahim
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Ruchira
authors.initials: R
authors.lastname: Chatterjee
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Sheraz
authors.initials: S
authors.lastname: Gul
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Franklin
authors.initials: F
authors.lastname: Fuller
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koroidov
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Aaron S
authors.initials: AS
authors.lastname: Brewster
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Rosalie
authors.initials: R
authors.lastname: Tran
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Roberto
authors.initials: R
authors.lastname: Alonso-Mori
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.|SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kroll
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Tara
authors.initials: T
authors.lastname: Michels-Clark
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Hartawan
authors.initials: H
authors.lastname: Laksmono
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.|Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Raymond G
authors.initials: RG
authors.lastname: Sierra
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Claudiu A
authors.initials: CA
authors.lastname: Stan
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Rana
authors.initials: R
authors.lastname: Hussein
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Miao
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Lacey
authors.initials: L
authors.lastname: Douthit
authors.affiliation: Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Kubin
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Casper
authors.initials: C
authors.lastname: de Lichtenberg
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Pham
authors.initials: P
authors.lastname: Long Vo
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Håkan
authors.initials: H
authors.lastname: Nilsson
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Mun Hon
authors.initials: MH
authors.lastname: Cheah
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Shevela
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Claudio
authors.initials: C
authors.lastname: Saracini
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Mackenzie A
authors.initials: MA
authors.lastname: Bean
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Ina
authors.initials: I
authors.lastname: Seuffert
authors.affiliation: SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Dimosthenis
authors.initials: D
authors.lastname: Sokaras
authors.affiliation: SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Tsu-Chien
authors.initials: TC
authors.lastname: Weng
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Ernest
authors.initials: E
authors.lastname: Pastor
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Clemens
authors.initials: C
authors.lastname: Weninger
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Fransson
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Louise
authors.initials: L
authors.lastname: Lassalle
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.|Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bräuer
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
authors.forename: Pierre
authors.initials: P
authors.lastname: Aller
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Docker
authors.affiliation: National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA.
authors.forename: Babak
authors.initials: B
authors.lastname: Andi
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
authors.forename: Allen M
authors.initials: AM
authors.lastname: Orville
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Glownia
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Silke
authors.initials: S
authors.lastname: Nelson
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Marcin
authors.initials: M
authors.lastname: Sikorski
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Diling
authors.initials: D
authors.lastname: Zhu
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Hunter
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Lane
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Andy
authors.initials: A
authors.lastname: Aquila
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Koglin
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Robinson
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Mengning
authors.initials: M
authors.lastname: Liang
authors.affiliation: LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Boutet
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Artem Y
authors.initials: AY
authors.lastname: Lyubimov
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Monarin
authors.initials: M
authors.lastname: Uervirojnangkoorn
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Moriarty
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Dorothee
authors.initials: D
authors.lastname: Liebschner
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.affiliation: STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK and CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
authors.forename: David G
authors.initials: DG
authors.lastname: Waterman
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
authors.forename: Gwyndaf
authors.initials: G
authors.lastname: Evans
authors.affiliation: Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Wernet
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Dobbek
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.|Department of Photon Science, Stanford University, Stanford, CA 94305.|Department of Structural Biology, Stanford University, Stanford, CA 94305.
authors.forename: William I
authors.initials: WI
authors.lastname: Weis
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.|Department of Photon Science, Stanford University, Stanford, CA 94305.
authors.forename: Axel T
authors.initials: AT
authors.lastname: Brunger
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Petrus H
authors.initials: PH
authors.lastname: Zwart
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany.
authors.forename: Athina
authors.initials: A
authors.lastname: Zouni
authors.affiliation: Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.|Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE 75237 Uppsala, Sweden.
authors.forename: Johannes
authors.initials: J
authors.lastname: Messinger
authors.affiliation: Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Uwe
authors.initials: U
authors.lastname: Bergmann
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Nicholas K
authors.initials: NK
authors.lastname: Sauter
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Kern
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Vittal K
authors.initials: VK
authors.lastname: Yachandra
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Junko
authors.initials: J
authors.lastname: Yano
mesh_terms: D000641:Ammonia / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003460:Crystallization; D000458:Cyanobacteria / Q000737:chemistry*; D004583:Electrons; D007834:Lasers; D008345:Manganese / Q000378:metabolism; D008958:Models, Molecular; D010100:Oxygen / Q000378:metabolism; D045332:Photosystem II Protein Complex / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity; D013696:Temperature; D014867:Water / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D045332:Photosystem II Protein Complex; D014867:Water; D008345:Manganese; D000641:Ammonia; D010100:Oxygen