6jy4 - Revision history

OCA at 10:21, 22 November 2023

OCA — Wed, 22 Nov 2023 10:21:42 GMT

←Older revision		Revision as of 10:21, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jy4' size='340' side='right'caption='[[6jy4]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6jy4' size='340' side='right'caption='[[6jy4]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jy4]] is a 13 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=6JY4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JY4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jy4]] is a 10 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=6JY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JY4 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=CQX:(2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol'>CQX</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</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=ZN:ZINC+ION'>ZN</scene~~></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]] 1.95Å</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></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=CQX:(2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol'>CQX</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jy3\|6jy3]]</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=6jy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jy4 OCA], [https://pdbe.org/6jy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jy4 RCSB], [https://www.ebi.ac.uk/pdbsum/6jy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jy4 ProSAT]</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=6jy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jy4 OCA], [~~http~~://pdbe.org/6jy4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jy4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jy4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jy4 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.	+	[https://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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6jy4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jy4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
-	[[Category: Cytochrome-c oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Muramoto, K]]	+	[[Category: Muramoto K]]
-	[[Category: Shinzawa-Itoh, K]]	+	[[Category: Shinzawa-Itoh K]]
-	~~[[Category: Fully reduced]]~~	+
-	~~[[Category: Monomer]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:08, 2 October 2019

OCA — Wed, 02 Oct 2019 11:08:29 GMT

←Older revision		Revision as of 11:08, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jy4 is ~~ON HOLD until Paper~~ Publication	+	==Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State==
		+	<StructureSection load='6jy4' size='340' side='right'caption='[[6jy4]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jy4]] is a 13 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=6JY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JY4 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=CQX:(2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol'>CQX</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</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=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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jy3\|6jy3]]</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=6jy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jy4 OCA], [http://pdbe.org/6jy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jy4 RCSB], [http://www.ebi.ac.uk/pdbsum/6jy4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jy4 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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytochrome c oxidase (CcO), a membrane enzyme in the respiratory chain, catalyzes oxygen reduction by coupling electron and proton transfer through the enzyme with a proton pump across the membrane. In all crystals reported to date, bovine CcO exists as a dimer with the same intermonomer contacts, whereas CcOs and related enzymes from prokaryotes exist as monomers. Recent structural analyses of the mitochondrial respiratory supercomplex revealed that CcO monomer associates with complex I and complex III, indicating that the monomeric state is functionally important. In this study, we prepared monomeric and dimeric bovine CcO, stabilized using amphipol, and showed that the monomer had high activity. In addition, using a newly synthesized detergent, we determined the oxidized and reduced structures of monomer with resolutions of 1.85 and 1.95 A, respectively. Structural comparison of the monomer and dimer revealed that a hydrogen bond network of water molecules is formed at the entry surface of the proton transfer pathway, termed the K-pathway, in monomeric CcO, whereas this network is altered in dimeric CcO. Based on these results, we propose that the monomer is the activated form, whereas the dimer can be regarded as a physiological standby form in the mitochondrial membrane. We also determined phospholipid structures based on electron density together with the anomalous scattering effect of phosphorus atoms. Two cardiolipins are found at the interface region of the supercomplex. We discuss formation of the monomeric CcO, dimeric CcO, and supercomplex, as well as their role in regulation of CcO activity.

-	~~Authors:~~ Shinzawa-Itoh, K., ~~Muramoto~~, K.	+	Monomeric structure of an active form of bovine cytochrome c oxidase.,Shinzawa-Itoh K, Sugimura T, Misaki T, Tadehara Y, Yamamoto S, Hanada M, Yano N, Nakagawa T, Uene S, Yamada T, Aoyama H, Yamashita E, Tsukihara T, Yoshikawa S, Muramoto K Proc Natl Acad Sci U S A. 2019 Sep 18. pii: 1907183116. doi:, 10.1073/pnas.1907183116. PMID:31533957<ref>PMID:31533957</ref>

-	~~Description: Monomeric Form~~ of ~~Bovine Heart Cytochrome c Oxidase in~~ the ~~Fully Reduced State~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Shinzawa~~-~~Itoh, K~~]]	+	<div class="pdbe-citations 6jy4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Cytochrome-c oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Muramoto, K]]		[[Category: Muramoto, K]]
		+	[[Category: Shinzawa-Itoh, K]]
		+	[[Category: Fully reduced]]
		+	[[Category: Monomer]]
		+	[[Category: Oxidoreductase]]

OCA at 05:02, 26 June 2019

OCA — Wed, 26 Jun 2019 05:02:22 GMT

←Older revision		Revision as of 05:02, 26 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jy4 is ON HOLD	+	The entry 6jy4 is ON HOLD until Paper Publication

	Authors: Shinzawa-Itoh, K., Muramoto, K.		Authors: Shinzawa-Itoh, K., Muramoto, K.

OCA: Protected "6jy4" [edit=sysop:move=sysop]

OCA — Wed, 01 May 2019 07:01:55 GMT

Protected "6jy4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:01, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jy4 is ON HOLD Authors: Shinzawa-Itoh, K., Muramoto, K. Description: Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced Stat...

OCA — Wed, 01 May 2019 07:01:54 GMT

New page: '''Unreleased structure''' The entry 6jy4 is ON HOLD Authors: Shinzawa-Itoh, K., Muramoto, K. Description: Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced Stat...

New page

'''Unreleased structure'''

The entry 6jy4 is ON HOLD

Authors: Shinzawa-Itoh, K., Muramoto, K.

Description: Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State
[[Category: Unreleased Structures]]
[[Category: Shinzawa-Itoh, K]]
[[Category: Muramoto, K]]