Structure of photosystem II and substrate binding at room temperature

Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin D.; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Vo Pham, Long; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

doi:10.1038/nature20161

Title: Structure of photosystem II and substrate binding at room temperature

Journal Article · 20 November 2016 · Nature (London)

DOI: https://doi.org/10.1038/nature20161 · OSTI ID:1361141

Young, Iris D.; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin D.; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Vo Pham, Long more »

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1361141

Alternate ID(s):: OSTI ID: 1376142; OSTI ID: 1379614

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7633 Vol. 540; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II Yamaguchi, K.; Shoji, M.; Isobe, H. Molecular Physics, Vol. 117, Issue 17 https://doi.org/10.1080/00268976.2018.1552799	journal	December 2018
Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II Yamaguchi, Kizashi; Yamanaka, Shusuke; Isobe, Hiroshi Physiologia Plantarum, Vol. 166, Issue 1 https://doi.org/10.1111/ppl.12960	journal	March 2019
Water oxidation in photosystem II Lubitz, Wolfgang; Chrysina, Maria; Cox, Nicholas Photosynthesis Research, Vol. 142, Issue 1 https://doi.org/10.1007/s11120-019-00648-3	journal	June 2019
What Mn K _β spectroscopy reveals concerning the oxidation states of the Mn cluster in photosystem II Petrie, Simon; Stranger, Rob; Pace, Ron J. Phys. Chem. Chem. Phys., Vol. 19, Issue 40 https://doi.org/10.1039/c7cp04797e	journal	January 2017
Local Structural Modification of Ca2+-Depleted Photosystem II Detected by Proton Matrix ENDOR Nagashima, Hiroki; Mino, Hiroyuki Applied Magnetic Resonance, Vol. 49, Issue 8 https://doi.org/10.1007/s00723-018-1006-1	journal	April 2018
Perspective: Opportunities for ultrafast science at SwissFEL Abela, Rafael; Beaud, Paul; van Bokhoven, Jeroen A. Structural Dynamics, Vol. 4, Issue 6 https://doi.org/10.1063/1.4997222	journal	November 2017
Using sound pulses to solve the crystal-harvesting bottleneck Samara, Yasmin N.; Brennan, Haley M.; McCarthy, Liam Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 10 https://doi.org/10.1107/s2059798318011506	journal	October 2018
Short-wavelength free-electron laser sources and science: a review Seddon, E. A.; Clarke, J. A.; Dunning, D. J. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-00596	text	January 2017
Unequal misses during the flash-induced advancement of photosystem II: effects of the S state and acceptor side cycles Pham, Long Vo; Janna Olmos, Julian David; Chernev, Petko Photosynthesis Research, Vol. 139, Issue 1-3 https://doi.org/10.1007/s11120-018-0574-0	journal	September 2018
Radiation damage in protein crystallography at X-ray free-electron lasers Nass, Karol Jan Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a2 https://doi.org/10.1107/s2053273317085497	journal	December 2017
Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W. ACS Energy Letters, Vol. 2, Issue 2 https://doi.org/10.1021/acsenergylett.6b00626	journal	January 2017
Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability Gorel, Alexander; Motomura, Koji; Fukuzawa, Hironobu Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00754-7	journal	October 2017
Radiation damage in protein crystallography at X-ray free-electron lasers Nass, Karol Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2 https://doi.org/10.1107/s2059798319000317	journal	January 2019
Rationalizing the 2.25 Å Resolution Crystal Structure of the Water Oxidising Complex of Photosystem II in the S ₃ State Petrie, Simon; Stranger, Rob; Pace, Ron J. ChemPhysChem, Vol. 18, Issue 20 https://doi.org/10.1002/cphc.201700640	journal	August 2017
A Gas‐Phase Ca _n Mn _{4− n} O ₄ ⁺ Cluster Model for the Oxygen‐Evolving Complex of Photosystem II Mauthe, Silvia; Fleischer, Irene; Bernhardt, Thorsten M. Angewandte Chemie https://doi.org/10.1002/ange.201903738	journal	May 2019
Efficient hydrogen production using photosystem I enhanced by artificial light harvesting dye Nagakawa, Haruki; Takeuchi, Ayano; Takekuma, Yuya Photochemical & Photobiological Sciences, Vol. 18, Issue 2 https://doi.org/10.1039/c8pp00426a	journal	January 2019
Structural isomers of the S ₂ state in photosystem II: do they exist at room temperature and are they important for function? Chatterjee, Ruchira; Lassalle, Louise; Gul, Sheraz Physiologia Plantarum, Vol. 166, Issue 1 https://doi.org/10.1111/ppl.12947	journal	March 2019
Temperature dependence of protein-water interactions in a gated yeast aquaporin Aponte-Santamaría, Camilo; Fischer, Gerhard; Båth, Petra Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-04180-z	journal	June 2017
Photonics and Optoelectronics with Bacteria: Making Materials from Photosynthetic Microorganisms Milano, Francesco; Punzi, Angela; Ragni, Roberta Advanced Functional Materials, Vol. 29, Issue 21 https://doi.org/10.1002/adfm.201805521	journal	December 2018
Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S ₃ State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å Petrie, Simon; Stranger, Robert; Pace, Ron J. ChemPhysChem, Vol. 19, Issue 23 https://doi.org/10.1002/cphc.201800686	journal	October 2018
A synthetic manganese–calcium cluster similar to the catalyst of Photosystem II: challenges for biomimetic water oxidation Mousazade, Younes; Mohammadi, Mohammad Reza; Bagheri, Robabeh Dalton Transactions https://doi.org/10.1039/d0dt00536c	journal	January 2020
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate Tosha, Takehiko; Nomura, Takashi; Nishida, Takuma Nature Communications, Vol. 8, Article No. 1585 https://doi.org/10.1038/s41467-017-01702-1	journal	November 2017
Pentanuclear iron catalysts for water oxidation: substituents provide two routes to control onset potentials Praneeth, Vijayendran K. K.; Kondo, Mio; Okamura, Masaya Chemical Science, Vol. 10, Issue 17 https://doi.org/10.1039/c9sc00678h	journal	January 2019
Co-existence of ferro- and antiferromagnetic interactions in a hexanuclear mixed-valence CoIII2MnII2MnIV2 cluster sustained by a multidentate Schiff base ligand Stetsiuk, Oleh; Synytsia, Valentyn; Petrusenko, Svitlana R. Dalton Transactions, Vol. 48, Issue 31 https://doi.org/10.1039/c9dt02503k	journal	January 2019
Dynamic pH‐induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen Carius, Anke B.; Rogne, Per; Duchoslav, Miloš Physiologia Plantarum, Vol. 166, Issue 1 https://doi.org/10.1111/ppl.12948	journal	March 2019
XFELs for structure and dynamics in biology Spence, J. C. H. IUCrJ, Vol. 4, Issue 4 https://doi.org/10.1107/S2052252517005760	journal	May 2017
How to make an efficient and robust molecular catalyst for water oxidation Garrido-Barros, Pablo; Gimbert-Suriñach, Carolina; Matheu, Roc Chemical Society Reviews, Vol. 46, Issue 20 https://doi.org/10.1039/c7cs00248c	journal	January 2017
Colloidal Fe ^III , Mn ^III , Co ^III , and Cu ^II Hydroxides Stabilized by Starch as Catalysts of Water Oxidation Reaction with One Electron Oxidant Ru(bpy) ₃ ³⁺ Chikunov, Andrei S.; Taran, Oxana P.; Pyshnaya, Inna A. ChemPhysChem, Vol. 20, Issue 3 https://doi.org/10.1002/cphc.201800957	journal	January 2019
Multi-wavelength anomalous diffraction de novo phasing using a two-colour X-ray free-electron laser with wide tunability Gorel, Alexander; Motomura, Koji; Fukuzawa, Hironobu Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00754-7	journal	October 2017
Sample delivery for serial crystallography at free-electron lasers and synchrotrons Grünbein, Marie Luise; Nass Kovacs, Gabriela Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2 https://doi.org/10.1107/S205979831801567X	journal	January 2019
Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy Woodhouse, Joyce; Nass Kovacs, Gabriela; Coquelle, Nicolas Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14537-0	journal	February 2020
Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals Wolff, Alexander M.; Young, Iris D.; Sierra, Raymond G. IUCrJ, Vol. 7, Issue 2 https://doi.org/10.1107/s205225252000072x	journal	February 2020
Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II Yamaguchi, Kizashi; Shoji, Mitsuo; Isobe, Hiroshi Taylor & Francis https://doi.org/10.6084/m9.figshare.5909185.v1	text	January 2018
Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II Yamaguchi, Kizashi; Shoji, Mitsuo; Isobe, Hiroshi Taylor & Francis https://doi.org/10.6084/m9.figshare.5909185	text	January 2018
A novel chlorophyll protein complex in the repair cycle of photosystem II Weisz, Daniel A.; Johnson, Virginia M.; Niedzwiedzki, Dariusz M. Proceedings of the National Academy of Sciences, Vol. 116, Issue 43 https://doi.org/10.1073/pnas.1909644116	journal	October 2019
Recent Advances in Ultrafast Structural Techniques Sciaini, Germán Applied Sciences, Vol. 9, Issue 7 https://doi.org/10.3390/app9071427	journal	April 2019
A tool for visualizing protein motions in time-resolved crystallography Cecilia, Wickstrand,; Gergely, Katona,; Takanori, Nakane, ETH Zurich https://doi.org/10.3929/ethz-b-000409850	text	January 2020
Manganese(II) complexes with Bn-tpen as powerful catalysts of cyclohexene oxidation Rydel-Ciszek, Katarzyna; Charczuk, Maria; Pacześniak, Tomasz Chemical Papers, Vol. 71, Issue 11 https://doi.org/10.1007/s11696-017-0201-0	journal	May 2017
Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II Yamaguchi, K.; Shoji, M.; Isobe, H. Taylor & Francis https://doi.org/10.6084/m9.figshare.7423610.v1	text	January 2018
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
Where is crystallography going? Grimes, Jonathan M.; Hall, David R.; Ashton, Alun W. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317016709	journal	February 2018
Inner-shell X-ray absorption spectra of the cationic series NH _y ⁺ ( y = 0–3) Bari, Sadia; Inhester, Ludger; Schubert, Kaja Physical Chemistry Chemical Physics, Vol. 21, Issue 30 https://doi.org/10.1039/c9cp02864a	journal	January 2019
Across the Board: Licheng Sun on the Mechanism of O−O Bond Formation in Photosystem II Zhang, BiaoBiao; Sun, Licheng ChemSusChem, Vol. 12, Issue 14 https://doi.org/10.1002/cssc.201901438	journal	June 2019
Why we need to know the structure of phosphorylated chloroplast light-harvesting complex II Allen, John F. Physiologia Plantarum, Vol. 161, Issue 1 https://doi.org/10.1111/ppl.12577	journal	May 2017
On the photocatalytic cycle of water splitting with small manganese oxides and the roles of water clusters as direct sources of oxygen molecules Yamamoto, Kentaro; Takatsuka, Kazuo Physical Chemistry Chemical Physics, Vol. 20, Issue 9 https://doi.org/10.1039/c7cp07171j	journal	January 2018
Hydrophilicity and oxophilicity of the isolated CaMn ₄ O ₅ cationic cluster modeling inorganic core of the oxygen-evolving complex Zhang, Yufei; Masuzaki, Daigo; Mafuné, Fumitaka Chemical Communications, Vol. 55, Issue 95 https://doi.org/10.1039/c9cc07818e	journal	January 2019
Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula Shoji, Mitsuo; Isobe, Hiroshi; Tanaka, Ayako ChemPhotoChem, Vol. 2, Issue 3 https://doi.org/10.1002/cptc.201700162	journal	December 2017
Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources Schmidt, Marius International Journal of Molecular Sciences, Vol. 20, Issue 6 https://doi.org/10.3390/ijms20061401	journal	March 2019
Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals Casadei, Cecilia M.; Nass, Karol; Barty, Anton Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-04823	text	January 2019
Effect of sucrose-bound polynuclear iron oxyhydroxide nanoparticles on the efficiency of electron transport in the photosystem II membranes Semin, B. К.; Davletshina, L. N.; Rubin, A. B. Photosynthesis Research, Vol. 142, Issue 1 https://doi.org/10.1007/s11120-019-00647-4	journal	May 2019
Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography Olmos, Jose L.; Pandey, Suraj; Martin-Garcia, Jose M. BMC Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s12915-018-0524-5	journal	May 2018
Water oxidation by a manganese–potassium cluster: Mn oxide as a kinetically dominant “true” catalyst for water oxidation Mousazade, Younes; Mohammadi, Mohammad Reza; Chernev, Petko Catalysis Science & Technology, Vol. 8, Issue 17 https://doi.org/10.1039/c8cy01151f	journal	January 2018
Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II Yamaguchi, Kizashi; Shoji, Mitsuo; Isobe, Hiroshi Molecular Physics, Vol. 116, Issue 5-6 https://doi.org/10.1080/00268976.2018.1428375	journal	December 2017
Significance of hydrogen bonding networks in the proton-coupled electron transfer reactions of photosystem II from a quantum-mechanics perspective Chai, Jun; Zheng, Zhaoyang; Pan, Hui Physical Chemistry Chemical Physics, Vol. 21, Issue 17 https://doi.org/10.1039/c9cp00868c	journal	January 2019
Perspective: Opportunities for ultrafast science at SwissFEL Abela, Rafael; Beaud, Paul; Van Bokhoven, Jeroen A. AIP Publishing https://doi.org/10.7892/boris.114739	text	January 2017
Perspective: Opportunities for ultrafast science at SwissFEL Abela, Rafael; Beaud, Paul; Van Bokhoven, Jeroen A. ETH Zurich https://doi.org/10.3929/ethz-b-000231826	text	January 2017
Unequal misses during the flash-induced advancement of photosystem II: effects of the S state and acceptor side cycles Pham, Long Vo; Janna Olmos, Julian David; Chernev, Petko Photosynthesis Research, Vol. 139, Issue 1-3 https://doi.org/10.1007/s11120-018-0574-0	journal	September 2018
Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster Guo, Zhanjun; He, Jiayuan; Barry, Bridgette A. Proceedings of the National Academy of Sciences, Vol. 115, Issue 22 https://doi.org/10.1073/pnas.1800758115	journal	May 2018
Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II Weisz, Daniel A.; Gross, Michael L.; Pakrasi, Himadri B. Science Advances, Vol. 3, Issue 11 https://doi.org/10.1126/sciadv.aao3013	journal	November 2017

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