4rvy: Difference between revisions

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-'''Unreleased structure'''
-The entry 4rvy is ON HOLD
+==Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)==
+<StructureSection load='4rvy' size='340' side='right'caption='[[4rvy]], [[Resolution|resolution]] 5.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4rvy]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4q54 4q54]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RVY 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]] 5.5&#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=CA:CALCIUM+ION'>CA</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=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=MG:MAGNESIUM+ION'>MG</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></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=4rvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvy OCA], [https://pdbe.org/4rvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rvy RCSB], [https://www.ebi.ac.uk/pdbsum/4rvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rvy ProSAT]</span></td></tr>
+</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 ==
+Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 A resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
-Authors: Kupitz, C., Basu, S., Grotjohann, I., Fromme, R., Zatsepin, N., Rendek, K.N., Hunter, M. , Shoeman, R.L., White, T. A. , Wang, D., James, D., Yang, J-H., Cobb, D.E., Reeder,B., Sierra, R.G., Liu,H., Barty,A., Aquila, A., Deponte, D., Kirian, R., Bari, S., Bergkamp, J.J., Beyerlein, K., Bogan, M.J., Caleman, C., Chao,T-C., Conrad, C.E., Davis, K.M., Fleckenstein, H., Galli, L., Hau Riege, S.P., Kassemeyer,, Laksmono, H., Liang, M., Lomb, L., Marchesini, S., Martin, A.V., Messerschmidt, M., Milathianaki, D., Nass, K., Ros, A., Roy Chowdhury, S., Schmidt, K, Seibert, M., Steinbrener, J., Stellato, F., Yan, L., Yoon, C., Moore, T.A., Moore, A.L., Pushkar, Y., Williams, G.J., Boutet, S., Doak
+Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.,Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang JH, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, Chao TC, Conrad CE, Davis KM, Fleckenstein H, Galli L, Hau-Riege SP, Kassemeyer S, Laksmono H, Liang M, Lomb L, Marchesini S, Martin AV, Messerschmidt M, Milathianaki D, Nass K, Ros A, Roy-Chowdhury S, Schmidt K, Seibert M, Steinbrener J, Stellato F, Yan L, Yoon C, Moore TA, Moore AL, Pushkar Y, Williams GJ, Boutet S, Doak RB, Weierstall U, Frank M, Chapman HN, Spence JC, Fromme P Nature. 2014 Jul 9. doi: 10.1038/nature13453. PMID:25043005<ref>PMID:25043005</ref>
-Description: Serial Time resolved crystallography of Photosystem II using a femtosecond X ray laser The S state after two flashes(S3)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4rvy" 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__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermosynechococcus vestitus BP-1]]
+[[Category: Aquila A]]
+[[Category: Bari S]]
+[[Category: Barty A]]
+[[Category: Basu S]]
+[[Category: Bergkamp JJ]]
+[[Category: Beyerlein K]]
+[[Category: Bogan MJ]]
+[[Category: Boutet S]]
+[[Category: Caleman C]]
+[[Category: Chao T-C]]
+[[Category: Chapman HN]]
+[[Category: Cobb DE]]
+[[Category: Conrad CE]]
+[[Category: Davis KM]]
+[[Category: Deponte D]]
+[[Category: Doak RB]]
+[[Category: Fleckenstein H]]
+[[Category: Frank M]]
+[[Category: Fromme P]]
+[[Category: Fromme R]]
+[[Category: Galli L]]
+[[Category: Grotjohann I]]
+[[Category: Hau-Riege SP]]
+[[Category: Hunter M]]
+[[Category: James D]]
+[[Category: Kassemeyer S]]
+[[Category: Kirian R]]
+[[Category: Kupitz C]]
+[[Category: Laksmono H]]
+[[Category: Liang M]]
+[[Category: Liu H]]
+[[Category: Lomb L]]
+[[Category: Marchesini S]]
+[[Category: Martin AV]]
+[[Category: Messerschmidt M]]
+[[Category: Milathianaki D]]
+[[Category: Moore AL]]
+[[Category: Moore TA]]
+[[Category: Nass K]]
+[[Category: Pushkar Y]]
+[[Category: Reeder B]]
+[[Category: Rendek KN]]
+[[Category: Ros A]]
+[[Category: Roy-Chowdhury S]]
+[[Category: Schmidt K]]
+[[Category: Seibert M]]
+[[Category: Shoeman RL]]
+[[Category: Sierra RG]]
+[[Category: Spence JCH]]
+[[Category: Steinbrener J]]
+[[Category: Stellato F]]
+[[Category: Wang D]]
+[[Category: Weierstall U]]
+[[Category: White TA]]
+[[Category: Williams GJ]]
+[[Category: Yan L]]
+[[Category: Yang J-H]]
+[[Category: Yoon C]]
+[[Category: Zatsepin N]]