5x1b - Revision history

OCA at 07:21, 7 October 2020

OCA — Wed, 07 Oct 2020 07:21:44 GMT

←Older revision		Revision as of 07:21, 7 October 2020
Line 1:		Line 1:

	==CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center==		==CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center==
-	<StructureSection load='5x1b' size='340' side='right' caption='[[5x1b]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5x1b' size='340' side='right'caption='[[5x1b]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x1b]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1B OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X1B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x1b]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X1B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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=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=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x19\|5x19]], [[5x1f\|5x1f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x19\|5x19]], [[5x1f\|5x1f]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=5x1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1b OCA], [http://pdbe.org/5x1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1b RCSB], [http://www.ebi.ac.uk/pdbsum/5x1b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1b ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1b OCA], [http://pdbe.org/5x1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1b RCSB], [http://www.ebi.ac.uk/pdbsum/5x1b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/COX5B_BOVIN COX5B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex. [[http://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX6C_BOVIN COX6C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7C_BOVIN COX7C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. [[http://www.uniprot.org/uniprot/CX6B1_BOVIN CX6B1_BOVIN]] Connects the two COX monomers into the physiological dimeric form. [[http://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. [[http://www.uniprot.org/uniprot/COX41_BOVIN COX41_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/~~COX8B_BOVIN COX8B_BOVIN~~]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/~~CX7A1_BOVIN CX7A1_BOVIN~~]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN]] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.	+	[[http://www.uniprot.org/uniprot/COX5B_BOVIN COX5B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex. [[http://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX6C_BOVIN COX6C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. [[http://www.uniprot.org/uniprot/COX7C_BOVIN COX7C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/CX6B1_BOVIN CX6B1_BOVIN]] Connects the two COX monomers into the physiological dimeric form. [[http://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. [[http://www.uniprot.org/uniprot/COX41_BOVIN COX41_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/CX7A1_BOVIN CX7A1_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX8B_BOVIN COX8B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN]] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5x1b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x1b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Ago, H]]		[[Category: Ago, H]]
	[[Category: Baba, J]]		[[Category: Baba, J]]

OCA at 07:52, 6 December 2017

OCA — Wed, 06 Dec 2017 07:52:17 GMT

←Older revision		Revision as of 07:52, 6 December 2017
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/COX5B_BOVIN COX5B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex. [[http://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX6C_BOVIN COX6C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7C_BOVIN COX7C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. [[http://www.uniprot.org/uniprot/CX6B1_BOVIN CX6B1_BOVIN]] Connects the two COX monomers into the physiological dimeric form. [[http://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. [[http://www.uniprot.org/uniprot/COX41_BOVIN COX41_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX8B_BOVIN COX8B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/CX7A1_BOVIN CX7A1_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN]] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.		[[http://www.uniprot.org/uniprot/COX5B_BOVIN COX5B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex. [[http://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX6C_BOVIN COX6C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7C_BOVIN COX7C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. [[http://www.uniprot.org/uniprot/CX6B1_BOVIN CX6B1_BOVIN]] Connects the two COX monomers into the physiological dimeric form. [[http://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. [[http://www.uniprot.org/uniprot/COX41_BOVIN COX41_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX8B_BOVIN COX8B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/CX7A1_BOVIN CX7A1_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN]] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
		+	<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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x1b" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:06, 7 October 2017

OCA — Sat, 07 Oct 2017 11:06:09 GMT

←Older revision		Revision as of 11:06, 7 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x1b ~~is ON HOLD until Paper Publication~~	+	==CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center==
-		+	<StructureSection load='5x1b' size='340' side='right' caption='[[5x1b]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~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~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x1b]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X1B FirstGlance]. <br>
-	~~Description~~: ~~CO bound~~ cytochrome c oxidase ~~at 20 nsec after pump laser irradiation~~ to ~~release CO~~ from O2 reduction center	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
-	[[Category: ~~Yoshikawa~~, S]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x19\|5x19]], [[5x1f\|5x1f]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=5x1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1b OCA], [http://pdbe.org/5x1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1b RCSB], [http://www.ebi.ac.uk/pdbsum/5x1b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1b ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COX5B_BOVIN COX5B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex. [[http://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX6C_BOVIN COX6C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX7C_BOVIN COX7C_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. [[http://www.uniprot.org/uniprot/CX6B1_BOVIN CX6B1_BOVIN]] Connects the two COX monomers into the physiological dimeric form. [[http://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. [[http://www.uniprot.org/uniprot/COX41_BOVIN COX41_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX8B_BOVIN COX8B_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/CX7A1_BOVIN CX7A1_BOVIN]] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. [[http://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN]] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Cytochrome-c oxidase]]
		+	[[Category: Ago, H]]
	[[Category: Baba, J]]		[[Category: Baba, J]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
		+	[[Category: Eto, Y]]
		+	[[Category: Hatano, K]]
		+	[[Category: Hirata, K]]
	[[Category: Kimura, T]]		[[Category: Kimura, T]]
		+	[[Category: Komiya, R]]
		+	[[Category: Kubo, M]]
		+	[[Category: Kumasaka, T]]
		+	[[Category: Miyamoto, A]]
		+	[[Category: Murakami, H]]
	[[Category: Nomura, T]]		[[Category: Nomura, T]]
-	[[Category: ~~Yamamoto~~, M]]	+	[[Category: Ogura, T]]
-	[[Category: ~~Yanagisawa~~, S]]	+	[[Category: Owada, S]]
		+	[[Category: Sakaguchi, M]]
		+	[[Category: Shimada, A]]
	[[Category: Shinzawa-Itoh, K]]		[[Category: Shinzawa-Itoh, K]]
-	[[Category: Ago, H]]
-	[[Category: Kubo, M]]
-	[[Category: Shimada, A]]
	[[Category: Tono, K]]		[[Category: Tono, K]]
		+	[[Category: Tsukihara, T]]
		+	[[Category: Ueno, G]]
		+	[[Category: Yabashi, M]]
		+	[[Category: Yamaguchi, Y]]
		+	[[Category: Yamamoto, M]]
	[[Category: Yamashita, E]]		[[Category: Yamashita, E]]
-	[[Category: ~~Yabashi, M]]~~	+	[[Category: Yamashita, K]]
-	~~[[Category: Eto, Y]]~~	+
-	~~[[Category: Komiya, R]]~~	+
-	~~[[Category: Ogura, T]]~~	+
-	~~[[Category: Hatano~~, K]]	+
-	~~[[Category: Sakaguchi, M]]~~	+
-	~~[[Category: Miyamoto, A~~]]	+
	[[Category: Yan, J]]		[[Category: Yan, J]]
-	[[Category: ~~Owada~~, S]]	+	[[Category: Yanagisawa, S]]
-	[[Category: ~~Yamashita~~, K]]	+	[[Category: Yoshikawa, S]]
-	[[Category: ~~Murakami, H~~]]	+	[[Category: Cytochrome c oxidase]]
-	[[Category: ~~Kumasaka, T~~]]	+	[[Category: Membrane protein]]
-	[[Category: ~~Yamaguchi, Y~~]]	+	[[Category: Oxidoreductase]]
-	[[Category: ~~Tsukihara, T~~]]	+	[[Category: Proton pump]]
-	[[Category: ~~Hirata, K~~]]	+	[[Category: Time-resolved analysis]]
-	[[Category: ~~Ueno, G~~]]	+	[[Category: X-ray free electron laser]]

OCA at 10:19, 12 April 2017

OCA — Wed, 12 Apr 2017 10:19:12 GMT

←Older revision		Revision as of 10:19, 12 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x1b is ON HOLD	+	The entry 5x1b is ON HOLD until Paper Publication

	Authors: 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.		Authors: 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.

OCA at 20:04, 15 March 2017

OCA — Wed, 15 Mar 2017 20:04:32 GMT

←Older revision		Revision as of 20:04, 15 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yoshikawa, S]]		[[Category: Yoshikawa, S]]
		+	[[Category: Baba, J]]
		+	[[Category: Baba, S]]
	[[Category: Kimura, T]]		[[Category: Kimura, T]]
	[[Category: Nomura, T]]		[[Category: Nomura, T]]
Line 13:		Line 15:
	[[Category: Yanagisawa, S]]		[[Category: Yanagisawa, S]]
	[[Category: Shinzawa-Itoh, K]]		[[Category: Shinzawa-Itoh, K]]
		+	[[Category: Ago, H]]
	[[Category: Kubo, M]]		[[Category: Kubo, M]]
	[[Category: Shimada, A]]		[[Category: Shimada, A]]
-	[[Category: Eto, Y]]
-	[[Category: Ogura, T]]
-	[[Category: Hatano, K]]
-	[[Category: Owada, S]]
-	[[Category: Yamashita, K]]
-	[[Category: Murakami, H]]
-	[[Category: Kumasaka, T]]
-	[[Category: Hirata, K]]
-	[[Category: Ueno, G]]
-	[[Category: Baba, J]]
-	[[Category: Baba, S]]
-	[[Category: Ago, H]]
	[[Category: Tono, K]]		[[Category: Tono, K]]
	[[Category: Yamashita, E]]		[[Category: Yamashita, E]]
	[[Category: Yabashi, M]]		[[Category: Yabashi, M]]
		+	[[Category: Eto, Y]]
	[[Category: Komiya, R]]		[[Category: Komiya, R]]
		+	[[Category: Ogura, T]]
		+	[[Category: Hatano, K]]
	[[Category: Sakaguchi, M]]		[[Category: Sakaguchi, M]]
	[[Category: Miyamoto, A]]		[[Category: Miyamoto, A]]
	[[Category: Yan, J]]		[[Category: Yan, J]]
		+	[[Category: Owada, S]]
		+	[[Category: Yamashita, K]]
		+	[[Category: Murakami, H]]
		+	[[Category: Kumasaka, T]]
	[[Category: Yamaguchi, Y]]		[[Category: Yamaguchi, Y]]
	[[Category: Tsukihara, T]]		[[Category: Tsukihara, T]]
		+	[[Category: Hirata, K]]
		+	[[Category: Ueno, G]]

OCA at 15:34, 9 March 2017

OCA — Thu, 09 Mar 2017 15:34:10 GMT

←Older revision		Revision as of 15:34, 9 March 2017
Line 3:		Line 3:
	The entry 5x1b is ON HOLD		The entry 5x1b is ON HOLD

-	Authors: ~~Atsuhiro~~ Shimada, ~~Minoru~~ Kubo, ~~Seiki~~ Baba, ~~Keitaro~~ Yamashita, ~~Kunio~~ Hirata, Go Ueno, ~~Takashi~~ Nomura, ~~Tetsunari~~ Kimura, ~~Kyoko~~ Shinzawa-Itoh, ~~Junpei~~ Baba, ~~Keita~~ Hatano, ~~Yuki~~ Eto, ~~Akari~~ Miyamoto, ~~Hironori~~ Murakami, ~~Takashi~~ Kumasaka, ~~Shigeki~~ Owada, ~~Kensuke~~ Tono, ~~Makina~~ Yabashi, ~~Yoshihiro~~ Yamaguchi, ~~Sachiko~~ Yanagisawa, ~~Miyuki~~ Sakaguchi, ~~Takashi~~ Ogura, ~~Ryo~~ Komiya, ~~Jiwang~~ Yan, ~~Eiki~~ Yamashita, ~~Masaki~~ Yamamoto, ~~Hideo~~ Ago, ~~Shinya~~ Yoshikawa, ~~Tomitake~~ Tsukihara	+	Authors: 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.

-	Description: ~~The structure of~~ CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center	+	Description: CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Atsuhiro Shimada~~, ~~Minoru Kubo, Seiki Baba, Keitaro Yamashita~~, ~~Kunio Hirata, Go Ueno, Takashi~~ Nomura, ~~Tetsunari Kimura~~, ~~Kyoko~~ Shinzawa-Itoh, ~~Junpei Baba~~, ~~Keita Hatano~~, ~~Yuki~~ Eto, ~~Akari Miyamoto~~, ~~Hironori~~ Murakami, ~~Takashi~~ Kumasaka, ~~Shigeki Owada~~, ~~Kensuke Tono~~, ~~Makina Yabashi~~, ~~Yoshihiro Yamaguchi~~, ~~Sachiko Yanagisawa~~, ~~Miyuki Sakaguchi~~, ~~Takashi Ogura~~, ~~Ryo~~ Komiya, ~~Jiwang Yan~~, ~~Eiki Yamashita~~, ~~Masaki Yamamoto~~, ~~Hideo Ago~~, ~~Shinya Yoshikawa~~, ~~Tomitake Tsukihara~~]]	+	[[Category: Yoshikawa, S]]
		+	[[Category: Kimura, T]]
		+	[[Category: Nomura, T]]
		+	[[Category: Yamamoto, M]]
		+	[[Category: Yanagisawa, S]]
		+	[[Category: Shinzawa-Itoh, K]]
		+	[[Category: Kubo, M]]
		+	[[Category: Shimada, A]]
		+	[[Category: Eto, Y]]
		+	[[Category: Ogura, T]]
		+	[[Category: Hatano, K]]
		+	[[Category: Owada, S]]
		+	[[Category: Yamashita, K]]
		+	[[Category: Murakami, H]]
		+	[[Category: Kumasaka, T]]
		+	[[Category: Hirata, K]]
		+	[[Category: Ueno, G]]
		+	[[Category: Baba, J]]
		+	[[Category: Baba, S]]
		+	[[Category: Ago, H]]
		+	[[Category: Tono, K]]
		+	[[Category: Yamashita, E]]
		+	[[Category: Yabashi, M]]
		+	[[Category: Komiya, R]]
		+	[[Category: Sakaguchi, M]]
		+	[[Category: Miyamoto, A]]
		+	[[Category: Yan, J]]
		+	[[Category: Yamaguchi, Y]]
		+	[[Category: Tsukihara, T]]

OCA: Protected "5x1b" [edit=sysop:move=sysop]

OCA — Wed, 01 Feb 2017 17:10:35 GMT

Protected "5x1b" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:10, 1 February 2017

OCA: New page: '''Unreleased structure''' The entry 5x1b is ON HOLD Authors: Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyok...

OCA — Wed, 01 Feb 2017 17:10:32 GMT

New page: '''Unreleased structure''' The entry 5x1b is ON HOLD Authors: Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyok...

New page

'''Unreleased structure'''

The entry 5x1b is ON HOLD

Authors: Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyoko Shinzawa-Itoh, Junpei Baba, Keita Hatano, Yuki Eto, Akari Miyamoto, Hironori Murakami, Takashi Kumasaka, Shigeki Owada, Kensuke Tono, Makina Yabashi, Yoshihiro Yamaguchi, Sachiko Yanagisawa, Miyuki Sakaguchi, Takashi Ogura, Ryo Komiya, Jiwang Yan, Eiki Yamashita, Masaki Yamamoto, Hideo Ago, Shinya Yoshikawa, Tomitake Tsukihara

Description: The structure of CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center
[[Category: Unreleased Structures]]
[[Category: Atsuhiro Shimada, Minoru Kubo, Seiki Baba, Keitaro Yamashita, Kunio Hirata, Go Ueno, Takashi Nomura, Tetsunari Kimura, Kyoko Shinzawa-Itoh, Junpei Baba, Keita Hatano, Yuki Eto, Akari Miyamoto, Hironori Murakami, Takashi Kumasaka, Shigeki Owada, Kensuke Tono, Makina Yabashi, Yoshihiro Yamaguchi, Sachiko Yanagisawa, Miyuki Sakaguchi, Takashi Ogura, Ryo Komiya, Jiwang Yan, Eiki Yamashita, Masaki Yamamoto, Hideo Ago, Shinya Yoshikawa, Tomitake Tsukihara]]