4rvy: Difference between revisions

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-'''Unreleased structure'''
+==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 38 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RVY FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvy OCA], [http://pdbe.org/4rvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rvy RCSB], [http://www.ebi.ac.uk/pdbsum/4rvy PDBsum]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref>  [[http://www.uniprot.org/uniprot/PSBB_THEEB PSBB_THEEB]] One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01495]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>  [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) concentrations.[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBC_THEEB PSBC_THEEB]] One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01496]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>  [[http://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref>  [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:17967798</ref>  [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]
+<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.
-The entry 4rvy is ON HOLD
+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>
-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, S., 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., D
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)
+<div class="pdbe-citations 4rvy" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
-[[Category: Liang, M]]
+<references/>
-[[Category: Caleman, C]]
+__TOC__
-[[Category: Galli, L]]
+</StructureSection>
-[[Category: Barty, A]]
+[[Category: Photosystem II]]
-[[Category: Yang, J.-H]]
+[[Category: Thermosynechococcus elongatus]]
-[[Category: Shoeman, R.L]]
-[[Category: Chao, T.-C]]
-[[Category: Stellato, F]]
-[[Category: Seibert, M]]
-[[Category: Bergkamp, J.J]]
-[[Category: Moore, T.A]]
-[[Category: Nass, K]]
-[[Category: Wang, D]]
-[[Category: Moore, A.L]]
-[[Category: Hau-Riege, S.P]]
-[[Category: Ros, A]]
-[[Category: Pushkar, Y]]
-[[Category: Marchesini, S]]
-[[Category: Conrad, C.E]]
-[[Category: White, T.A]]
-[[Category: Yoon, C]]
-[[Category: Kupitz, C]]
-[[Category: Schmidt, K]]
-[[Category: Lomb, L]]
-[[Category: Liu, H]]
-[[Category: D]]
-[[Category: Williams, G.J]]
 [[Category: Aquila, A]]
-[[Category: Zatsepin, N]]
-[[Category: Martin, A.V]]
-[[Category: Yan, L]]
-[[Category: Kirian, R]]
-[[Category: Fromme, R]]
-[[Category: Cobb, D.E]]
-[[Category: Boutet, S]]
-[[Category: Hunter, M]]
 [[Category: Bari, S]]
-[[Category: Messerschmidt, M]]
+[[Category: Barty, A]]
+[[Category: Basu, S]]
+[[Category: Bergkamp, J J]]
 [[Category: Beyerlein, K]]
+[[Category: Bogan, M J]]
+[[Category: Boutet, S]]
+[[Category: Caleman, C]]
+[[Category: Chao, T C]]
+[[Category: Chapman, H N]]
+[[Category: Cobb, D E]]
+[[Category: Conrad, C E]]
+[[Category: Davis, K M]]
+[[Category: Deponte, D]]
+[[Category: Doak, R B]]
+[[Category: Fleckenstein, H]]
+[[Category: Frank, M]]
+[[Category: Fromme, P]]
+[[Category: Fromme, R]]
+[[Category: Galli, L]]
 [[Category: Grotjohann, I]]
-[[Category: Sierra, R.G]]
+[[Category: Hau-Riege, S P]]
-[[Category: Roy-Chowdhury, S]]
+[[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, A V]]
+[[Category: Messerschmidt, M]]
 [[Category: Milathianaki, D]]
-[[Category: Basu, S]]
+[[Category: Moore, A L]]
-[[Category: Rendek, K.N]]
+[[Category: Moore, T A]]
-[[Category: Bogan, M.J]]
+[[Category: Nass, K]]
-[[Category: Davis, K.M]]
+[[Category: Pushkar, Y]]
-[[Category: Kassemeyer, S]]
 [[Category: Reeder, B]]
-[[Category: Fleckenstein, H]]
+[[Category: Rendek, K N]]
-[[Category: Deponte, D]]
+[[Category: Ros, A]]
+[[Category: Roy-Chowdhury, S]]
+[[Category: Schmidt, K]]
+[[Category: Seibert, M]]
+[[Category: Shoeman, R L]]
+[[Category: Sierra, R G]]
+[[Category: Spence, J C.H]]
 [[Category: Steinbrener, J]]
+[[Category: Stellato, F]]
+[[Category: Wang, D]]
+[[Category: Weierstall, U]]
+[[Category: White, T A]]
+[[Category: Williams, G J]]
+[[Category: Yan, L]]
+[[Category: Yang, J H]]
+[[Category: Yoon, C]]
+[[Category: Zatsepin, N]]
+[[Category: Electron transport]]
+[[Category: Free electron laser]]
+[[Category: Membrane]]
+[[Category: Oxidoreductase]]
+[[Category: Photosystem ii]]
+[[Category: Time resolved]]