7tih - Revision history

OCA at 17:04, 18 October 2023

OCA — Wed, 18 Oct 2023 17:04:42 GMT

←Older revision		Revision as of 17:04, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7tih]] 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=7TIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TIH FirstGlance]. <br>		<table><tr><td colspan='2'>[[7tih]] 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=7TIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TIH FirstGlance]. <br>
-	</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=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=OH:HYDROXIDE+ION'>OH</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=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]] 2.35Å</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=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=OH:HYDROXIDE+ION'>OH</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=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=7tih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tih OCA], [https://pdbe.org/7tih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tih RCSB], [https://www.ebi.ac.uk/pdbsum/7tih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tih ProSAT]</span></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=7tih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tih OCA], [https://pdbe.org/7tih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tih RCSB], [https://www.ebi.ac.uk/pdbsum/7tih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tih ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex.	+	[https://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN] Subunits I, II and III form the functional core of the enzyme complex.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7tih" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7tih" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:25, 8 September 2022

OCA — Thu, 08 Sep 2022 06:25:51 GMT

←Older revision		Revision as of 06:25, 8 September 2022
Line 1:		Line 1:

-	====	+	==Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure==
-	<StructureSection load='7tih' size='340' side='right'caption='[[7tih]]' scene=''>	+	<StructureSection load='7tih' size='340' side='right'caption='[[7tih]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tih]] 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=7TIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TIH FirstGlance]. <br>
-	</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=7tih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tih OCA], [https://pdbe.org/7tih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tih RCSB], [https://www.ebi.ac.uk/pdbsum/7tih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tih ProSAT]</span></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=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=OH:HYDROXIDE+ION'>OH</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=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=7tih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tih OCA], [https://pdbe.org/7tih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tih RCSB], [https://www.ebi.ac.uk/pdbsum/7tih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tih ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN]] Subunits I, II and III form the functional core of the enzyme complex.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in the inner membrane of mitochondria. It contains four metal redox centers, two of which, CuB and heme a3, form the binuclear center (BNC), where dioxygen is reduced to water. Crystal structures of CcO in various forms have been reported, from which ligand-binding states of the BNC and conformations of the protein matrix surrounding it have been deduced to elucidate the mechanism by which the oxygen reduction chemistry is coupled to proton translocation. However, metal centers in proteins can be susceptible to X-ray-induced radiation damage, raising questions about the reliability of conclusions drawn from these studies. Here, we used microspectroscopy-coupled X-ray crystallography to interrogate how the structural integrity of bovine CcO in the fully oxidized state (O) is modulated by synchrotron radiation. Spectroscopic data showed that, upon X-ray exposure, O was converted to a hybrid O * state where all the four metal centers were reduced, but the protein matrix was trapped in the genuine O conformation and the ligands in the BNC remained intact. Annealing the O * crystal above the glass transition temperature induced relaxation of the O * structure to a new R * structure, wherein the protein matrix converted to the fully reduced R conformation with the exception of helix X, which partly remained in the O conformation because of incomplete dissociation of the ligands from the BNC. We conclude from these data that reevaluation of reported CcO structures obtained with synchrotron light sources is merited.
		+
		+	Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase.,Ishigami I, Russi S, Cohen A, Yeh SR, Rousseau DL J Biol Chem. 2022 Apr;298(4):101799. doi: 10.1016/j.jbc.2022.101799. Epub 2022, Mar 5. PMID:35257742<ref>PMID:35257742</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tih" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Cohen A]]
		+	[[Category: Ishigami I]]
		+	[[Category: Rousseau DL]]
		+	[[Category: Russi S]]
		+	[[Category: Yeh S-R]]

OCA at 10:47, 30 March 2022

OCA — Wed, 30 Mar 2022 10:47:58 GMT

←Older revision		Revision as of 10:47, 30 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7tih ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7tih' size='340' side='right'caption='[[7tih]]' scene=''>
-	~~Authors~~: ~~Ishigami, I~~.~~, Rousseau, D~~.~~L., Yeh, S~~.-R.~~, Russi, S~~.~~, Cohen, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure~~	+	</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=7tih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tih OCA], [https://pdbe.org/7tih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tih RCSB], [https://www.ebi.ac.uk/pdbsum/7tih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tih ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Cohen, A~~]]	+	__TOC__
-	[~~[Category~~: ~~Russi~~, S]]	+	</StructureSection>
-	[~~[Category~~: ~~Yeh~~, S.-R]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ishigami, I~~]]	+	[[Category: Z-disk]]
-	[[Category: ~~Rousseau, D.L~~]]	+

OCA at 06:29, 23 February 2022

OCA — Wed, 23 Feb 2022 06:29:10 GMT

←Older revision		Revision as of 06:29, 23 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7tih is ON HOLD	+	The entry 7tih is ON HOLD until Paper Publication

	Authors: Ishigami, I., Rousseau, D.L., Yeh, S.-R., Russi, S., Cohen, A.		Authors: Ishigami, I., Rousseau, D.L., Yeh, S.-R., Russi, S., Cohen, A.

OCA: Protected "7tih" [edit=sysop:move=sysop]

OCA — Wed, 19 Jan 2022 06:06:15 GMT

Protected "7tih" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:06, 19 January 2022

OCA: New page: '''Unreleased structure''' The entry 7tih is ON HOLD Authors: Ishigami, I., Rousseau, D.L., Yeh, S.-R., Russi, S., Cohen, A. Description: Structure of oxidized bovine cytochrome c oxid...

OCA — Wed, 19 Jan 2022 06:06:14 GMT

New page: '''Unreleased structure''' The entry 7tih is ON HOLD Authors: Ishigami, I., Rousseau, D.L., Yeh, S.-R., Russi, S., Cohen, A. Description: Structure of oxidized bovine cytochrome c oxid...

New page

'''Unreleased structure'''

The entry 7tih is ON HOLD

Authors: Ishigami, I., Rousseau, D.L., Yeh, S.-R., Russi, S., Cohen, A.

Description: Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure
[[Category: Unreleased Structures]]
[[Category: Cohen, A]]
[[Category: Russi, S]]
[[Category: Yeh, S.-R]]
[[Category: Ishigami, I]]
[[Category: Rousseau, D.L]]