5x1f: Difference between revisions

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-'''Unreleased structure'''
-The entry 5x1f is ON HOLD  until Paper Publication
+==CO bound cytochrome c oxidase without pump laser irradiation at 278K==
+<StructureSection load='5x1f' size='340' side='right'caption='[[5x1f]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5x1f]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X1F 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CHD:CHOLIC+ACID'>CHD</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEK:(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL+(5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE'>PEK</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</scene>, <scene name='pdbligand=PSC:(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM+4-OXIDE'>PSC</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5x1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1f OCA], [https://pdbe.org/5x1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x1f RCSB], [https://www.ebi.ac.uk/pdbsum/5x1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COX1_BOVIN COX1_BOVIN] Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1-3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bovine cytochrome c oxidase (CcO), a 420-kDa membrane protein, pumps protons using electrostatic repulsion between protons transferred through a water channel and net positive charges created by oxidation of heme a (Fe a ) for reduction of O2 at heme a3 (Fe a3). For this process to function properly, timing is essential: The channel must be closed after collection of the protons to be pumped and before Fe a oxidation. If the channel were to remain open, spontaneous backflow of the collected protons would occur. For elucidation of the channel closure mechanism, the opening of the channel, which occurs upon release of CO from CcO, is investigated by newly developed time-resolved x-ray free-electron laser and infrared techniques with nanosecond time resolution. The opening process indicates that CuB senses completion of proton collection and binds O2 before binding to Fe a3 to close the water channel using a conformational relay system, which includes CuB, heme a3, and a transmembrane helix, to block backflow of the collected protons.
-Authors:
+A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.,Shimada A, Kubo M, Baba S, Yamashita K, Hirata K, Ueno G, Nomura T, Kimura T, Shinzawa-Itoh K, Baba J, Hatano K, Eto Y, Miyamoto A, Murakami H, Kumasaka T, Owada S, Tono K, Yabashi M, Yamaguchi Y, Yanagisawa S, Sakaguchi M, Ogura T, Komiya R, Yan J, Yamashita E, Yamamoto M, Ago H, Yoshikawa S, Tsukihara T Sci Adv. 2017 Jul 14;3(7):e1603042. doi: 10.1126/sciadv.1603042. eCollection 2017, Jul. PMID:28740863<ref>PMID:28740863</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5x1f" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bos taurus]]
+[[Category: Large Structures]]
+[[Category: Ago H]]
+[[Category: Baba J]]
+[[Category: Baba S]]
+[[Category: Eto Y]]
+[[Category: Hatano K]]
+[[Category: Hirata K]]
+[[Category: Kimura T]]
+[[Category: Komiya R]]
+[[Category: Kubo M]]
+[[Category: Kumasaka T]]
+[[Category: Miyamoto A]]
+[[Category: Murakami H]]
+[[Category: Nomura T]]
+[[Category: Ogura T]]
+[[Category: Owada S]]
+[[Category: Sakaguchi M]]
+[[Category: Shimada A]]
+[[Category: Shinzawa-Itoh K]]
+[[Category: Tono K]]
+[[Category: Tsukihara T]]
+[[Category: Ueno G]]
+[[Category: Yabashi M]]
+[[Category: Yamaguchi Y]]
+[[Category: Yamamoto M]]
+[[Category: Yamashita E]]
+[[Category: Yamashita K]]
+[[Category: Yan J]]
+[[Category: Yanagisawa S]]
+[[Category: Yoshikawa S]]