7rf2: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==== | ==RT XFEL structure of dark-stable state of Photosystem II (0F, S1 rich) at 2.08 Angstrom== | ||
<StructureSection load='7rf2' size='340' side='right'caption='[[7rf2]]' scene=''> | <StructureSection load='7rf2' size='340' side='right'caption='[[7rf2]], [[Resolution|resolution]] 2.08Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[7rf2]] 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=7RF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RF2 FirstGlance]. <br> | ||
</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=7rf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rf2 OCA], [https://pdbe.org/7rf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rf2 RCSB], [https://www.ebi.ac.uk/pdbsum/7rf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rf2 ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.08Å</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=OEX:CA-MN4-O5+CLUSTER'>OEX</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>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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=7rf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rf2 OCA], [https://pdbe.org/7rf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rf2 RCSB], [https://www.ebi.ac.uk/pdbsum/7rf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rf2 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PSBA1_THEVB PSBA1_THEVB] Photosystem II (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. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 A structure obtained by averaging all the S states and refining the data of various time points during the S(2) to S(3) transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons. | |||
Structural dynamics in the water and proton channels of photosystem II during the S(2) to S(3) transition.,Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J Nat Commun. 2021 Nov 11;12(1):6531. doi: 10.1038/s41467-021-26781-z. PMID:34764256<ref>PMID:34764256</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7rf2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
*[[Photosystem II 3D structures|Photosystem II 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermosynechococcus vestitus BP-1]] | ||
[[Category: Adams PD]] | |||
[[Category: Alonso-Mori R]] | |||
[[Category: Batyuk A]] | |||
[[Category: Bergmann U]] | |||
[[Category: Bhowmick A]] | |||
[[Category: Bogacz I]] | |||
[[Category: Bolotovski R]] | |||
[[Category: Brewster AS]] | |||
[[Category: Carbajo S]] | |||
[[Category: Chatterjee R]] | |||
[[Category: Cheah MH]] | |||
[[Category: Chernev P]] | |||
[[Category: Dobbek H]] | |||
[[Category: Doyle MD]] | |||
[[Category: Fuller FD]] | |||
[[Category: Gul S]] | |||
[[Category: Holton JM]] | |||
[[Category: Hussein R]] | |||
[[Category: Ibrahim M]] | |||
[[Category: Kern J]] | |||
[[Category: Kim I-S]] | |||
[[Category: Lassalle L]] | |||
[[Category: Mendez D]] | |||
[[Category: Messinger J]] | |||
[[Category: Moriarty NW]] | |||
[[Category: Pham CC]] | |||
[[Category: Sauter NK]] | |||
[[Category: Simon PS]] | |||
[[Category: Sutherlin KD]] | |||
[[Category: Yachandra VK]] | |||
[[Category: Yano J]] | |||
[[Category: Young ID]] | |||
[[Category: Zouni A]] | |||
[[Category: De Lichtenberg C]] | |||