4q5p - Revision history

OCA at 17:28, 20 September 2023

OCA — Wed, 20 Sep 2023 17:28:24 GMT

←Older revision		Revision as of 17:28, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.87Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [https://pdbe.org/4q5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [https://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p 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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [https://pdbe.org/4q5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [https://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:44, 8 February 2023

OCA — Wed, 08 Feb 2023 07:44:27 GMT

←Older revision		Revision as of 07:44, 8 February 2023
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	<StructureSection load='4q5p' size='340' side='right'caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='4q5p' size='340' side='right'caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYC1, YJR048W, J1653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [https://pdbe.org/4q5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [https://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [~~http~~://pdbe.org/4q5p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.	+	[https://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Amacher, J F~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Madden, D R~~]]	+	[[Category: Amacher JF]]
-	[[Category: ~~Pletneva, E V~~]]	+	[[Category: Madden DR]]
-	[[Category: ~~Zhong, F~~]]	+	[[Category: Pletneva EV]]
-	[[Category: ~~Zhu, M Q~~]]	+	[[Category: Zhong F]]
-	[[Category: ~~Electron transport~~]]	+	[[Category: Zhu MQ]]

OCA at 12:14, 17 July 2019

OCA — Wed, 17 Jul 2019 12:14:33 GMT

←Older revision		Revision as of 12:14, 17 July 2019
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4q5p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4q5p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:55, 24 April 2019

OCA — Wed, 24 Apr 2019 08:55:03 GMT

←Older revision		Revision as of 08:55, 24 April 2019
Line 1:		Line 1:

	==Lysine-Ligated Yeast Iso-1 Cytochrome C==		==Lysine-Ligated Yeast Iso-1 Cytochrome C==
-	<StructureSection load='4q5p' size='340' side='right' caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='4q5p' size='340' side='right'caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYC1, YJR048W, J1653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [http://pdbe.org/4q5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [http://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [http://pdbe.org/4q5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [http://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Amacher, J F]]		[[Category: Amacher, J F]]
	[[Category: Madden, D R]]		[[Category: Madden, D R]]

OCA at 14:16, 27 April 2017

OCA — Thu, 27 Apr 2017 14:16:59 GMT

←Older revision		Revision as of 14:16, 27 April 2017
Line 1:		Line 1:
		+
	==Lysine-Ligated Yeast Iso-1 Cytochrome C==		==Lysine-Ligated Yeast Iso-1 Cytochrome C==
	<StructureSection load='4q5p' size='340' side='right' caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='4q5p' size='340' side='right' caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [http://www.ebi.ac.uk/pdbsum/4q5p PDBsum]</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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [http://pdbe.org/4q5p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [http://www.ebi.ac.uk/pdbsum/4q5p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4q5p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:44, 24 June 2015

OCA — Wed, 24 Jun 2015 06:44:00 GMT

←Older revision		Revision as of 06:44, 24 June 2015
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.		[[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	It has been suggested that the alkaline form of cytochrome c (cyt c) regulates function of this protein as an electron carrier in oxidative phosphorylation and as a peroxidase that reacts with cardiolipin (CL) during apoptosis. In this form, Met80, the native ligand to the heme iron, is replaced by a Lys. While it has become clear that the structure of cyt c changes, the extent and sequence of conformational rearrangements associated with this ligand replacement remain a subject of debate. Herein we report a high-resolution crystal structure of a Lys73-ligated cyt c conformation that reveals intricate change in the heme environment upon this switch in the heme iron ligation. The structure is surprisingly compact, and the heme coordination loop refolds into a beta-hairpin with a turn formed by the highly conserved residues Pro76 and Gly77. Repositioning of residue 78 modifies the intraprotein hydrogen-bonding network and, together with adjustments of residues 52 and 74, increases the volume of the heme pocket to allow for insertion of one of the CL acyl moieties next to Asn52. Derivatization of Cys78 with maleimide creates a solution mimic of the Lys-ligated cyt c that has enhanced peroxidase activity, adding support for a role of the Lys-ligated cyt c in the apoptotic mechanism. Experiments with the heme peptide microperoxidase-8 and engineered model proteins provide a thermodynamic rationale for the switch to Lys ligation upon perturbations in the protein scaffold.
		+
		+	A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch.,Amacher JF, Zhong F, Lisi GP, Zhu MQ, Alden SL, Hoke KR, Madden DR, Pletneva EV J Am Chem Soc. 2015 Jun 3. PMID:26038984<ref>PMID:26038984</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:51, 22 April 2015

OCA — Wed, 22 Apr 2015 12:51:52 GMT

←Older revision		Revision as of 12:51, 22 April 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Lysine-Ligated Yeast Iso-1 Cytochrome C==
-		+	<StructureSection load='4q5p' size='340' side='right' caption='[[4q5p]], [[Resolution\|resolution]] 1.87Å' scene=''>
-	~~The entry~~ 4q5p is ~~ON HOLD until Jul 22 2016~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4q5p]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q5P FirstGlance]. <br>
-	~~Authors~~: ~~Amacher, J~~.F.~~, Zhu, M~~.Q., ~~Zhong, F~~., ~~Pletneva, E~~.V., ~~Madden, D~~.R.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=4q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q5p RCSB], [http://www.ebi.ac.uk/pdbsum/4q5p PDBsum]</span></td></tr>
-	~~Description~~: ~~Lysine-Ligated Yeast Iso-1~~ Cytochrome C	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Amacher, J F]]
		+	[[Category: Madden, D R]]
		+	[[Category: Pletneva, E V]]
	[[Category: Zhong, F]]		[[Category: Zhong, F]]
-	[[Category: Zhu, M.Q]]	+	[[Category: Zhu, M Q]]
-	[[Category: ~~Amacher, J.F]]~~	+	[[Category: Electron transport]]
-	~~[[Category: Madden, D.R]]~~	+
-	~~[[Category: Pletneva, E.V~~]]	+

OCA at 08:03, 15 April 2015

OCA — Wed, 15 Apr 2015 08:03:09 GMT

←Older revision		Revision as of 08:03, 15 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4q5p is ON HOLD	+	The entry 4q5p is ON HOLD until Jul 22 2016

	Authors: Amacher, J.F., Zhu, M.Q., Zhong, F., Pletneva, E.V., Madden, D.R.		Authors: Amacher, J.F., Zhu, M.Q., Zhong, F., Pletneva, E.V., Madden, D.R.

OCA at 07:51, 12 February 2015

OCA — Thu, 12 Feb 2015 07:51:00 GMT

←Older revision		Revision as of 07:51, 12 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4q5p is ON HOLD ~~until Paper Publication~~	+	The entry 4q5p is ON HOLD

	Authors: Amacher, J.F., Zhu, M.Q., Zhong, F., Pletneva, E.V., Madden, D.R.		Authors: Amacher, J.F., Zhu, M.Q., Zhong, F., Pletneva, E.V., Madden, D.R.

OCA at 15:26, 24 December 2014

OCA — Wed, 24 Dec 2014 15:26:24 GMT

←Older revision		Revision as of 15:26, 24 December 2014
Line 6:		Line 6:

	Description: Lysine-Ligated Yeast Iso-1 Cytochrome C		Description: Lysine-Ligated Yeast Iso-1 Cytochrome C
		+	[[Category: Unreleased Structures]]
		+	[[Category: Zhong, F]]
		+	[[Category: Zhu, M.Q]]
		+	[[Category: Amacher, J.F]]
		+	[[Category: Madden, D.R]]
		+	[[Category: Pletneva, E.V]]