View source for 6dhf


==RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution==
<StructureSection load='6dhf' size='340' side='right'caption='[[6dhf]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6dhf]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.08&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6dhf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhf OCA], [https://pdbe.org/6dhf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhf RCSB], [https://www.ebi.ac.uk/pdbsum/6dhf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PSBJ_THEVB PSBJ_THEVB] One of the components of the core complex of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation.[HAMAP-Rule:MF_01305]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:22387395</ref> <ref>PMID:25006873</ref>   May play a regulatory role in PSII biogenesis.<ref>PMID:33846594</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle(1,2). The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex(3-7). This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 A). In addition, we report structures of two transient states at 150 and 400 micros, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2--&gt;S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

Structures of the intermediates of Kok's photosynthetic water oxidation clock.,Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK Nature. 2018 Nov;563(7731):421-425. doi: 10.1038/s41586-018-0681-2. Epub 2018 Nov, 7. PMID:30405241<ref>PMID:30405241</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6dhf" style="background-color:#fffaf0;"></div>

==See Also==
*[[Photosystem II 3D structures|Photosystem II 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermosynechococcus vestitus BP-1]]
[[Category: Adams PD]]
[[Category: Aller P]]
[[Category: Alonso-Mori R]]
[[Category: Batyuk A]]
[[Category: Bergmann U]]
[[Category: Boutet S]]
[[Category: Brewster AS]]
[[Category: Butryn A]]
[[Category: Carbajo S]]
[[Category: Chatterjee R]]
[[Category: Cheah MH]]
[[Category: Dobbek H]]
[[Category: Douthit L]]
[[Category: Fransson T]]
[[Category: Fuller FD]]
[[Category: Gul S]]
[[Category: Holton JM]]
[[Category: Hussein R]]
[[Category: Ibrahim M]]
[[Category: Kern J]]
[[Category: Koglin JE]]
[[Category: Kroll T]]
[[Category: Lassalle L]]
[[Category: Liang M]]
[[Category: Messinger J]]
[[Category: Moriarty NW]]
[[Category: Orville AM]]
[[Category: Pastor E]]
[[Category: Sauter NK]]
[[Category: Seufert I]]
[[Category: Shevela D]]
[[Category: Sierra RG]]
[[Category: Sokaras D]]
[[Category: Weninger C]]
[[Category: Wersig J]]
[[Category: Yachandra VK]]
[[Category: Yano J]]
[[Category: Young ID]]
[[Category: Zhang M]]
[[Category: Zouni A]]
[[Category: De Lichtenberg C]]