3wui - Revision history

OCA at 13:29, 8 November 2023

2023-11-08T13:29:39Z

←Older revision		Revision as of 13:29, 8 November 2023
Line 1:		Line 1:

	==Dimeric horse cytochrome c formed by refolding from molten globule state==		==Dimeric horse cytochrome c formed by refolding from molten globule state==
-	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]]' scene=''>	+	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' 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=3WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUI 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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [https://pdbe.org/3wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [https://www.ebi.ac.uk/pdbsum/3wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [https://pdbe.org/3wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [https://www.ebi.ac.uk/pdbsum/3wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE] 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. Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many proteins, including cytochrome c (cyt c), have been shown to form domain-swapped oligomers, but the factors governing the oligomerization process remain unrevealed. We obtained oligomers of cyt c by refolding cyt c from its acid molten globule state to neutral pH state under high protein and ion concentrations. The amount of oligomeric cyt c obtained depended on the nature of the anion (chaotropic or kosmotropic) in the solution: ClO4- (oligomers, 11% +/- 2% (heme unit)), SCN- (10% +/- 2%), I- (6% +/- 2%), NO3- (3% +/- 1%), Br- (2% +/- 1%), Cl- (2% +/- 1%), and SO42- (3% +/- 1%) for refolding of 2 mM cyt c (anion concentration 125 mM). Dimeric cyt c obtained by refolding from the molten globule state exhibited a domain-swapped structure, in which the C-terminal alpha-helices were exchanged between protomers. According to small-angle X-ray scattering measurements, approximately 25% of the cyt c molecules were dimerized in the molten globule state containing 125 mM ClO4-. These results indicate that a certain amount of molten globule state oligomers of cyt c convert to domain-swapped oligomers during refolding and that the intermolecular interactions necessary for domain swapping are present in the molten globule state.
		+
		+	Formation of Domain-Swapped Oligomer of Cytochrome c from Its Molten Globule State Oligomer.,Deshpande MS, Parui PP, Kamikubo H, Yamanaka M, Nagao S, Komori H, Kataoka M, Higuchi Y, Hirota S Biochemistry. 2014 Jul 9. PMID:24981551<ref>PMID:24981551</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3wui" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Deshpande MS]]		[[Category: Deshpande MS]]

OCA at 10:36, 31 August 2022

2022-08-31T10:36:09Z

←Older revision		Revision as of 10:36, 31 August 2022
Line 1:		Line 1:

	==Dimeric horse cytochrome c formed by refolding from molten globule state==		==Dimeric horse cytochrome c formed by refolding from molten globule state==
-	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>	+	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3wui]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [https://pdbe.org/3wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [https://www.ebi.ac.uk/pdbsum/3wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wc8\|3wc8]]</div></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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [https://pdbe.org/3wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [https://www.ebi.ac.uk/pdbsum/3wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE]] 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. Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Many proteins, including cytochrome c (cyt c), have been shown to form domain-swapped oligomers, but the factors governing the oligomerization process remain unrevealed. We obtained oligomers of cyt c by refolding cyt c from its acid molten globule state to neutral pH state under high protein and ion concentrations. The amount of oligomeric cyt c obtained depended on the nature of the anion (chaotropic or kosmotropic) in the solution: ClO4- (oligomers, 11% +/- 2% (heme unit)), SCN- (10% +/- 2%), I- (6% +/- 2%), NO3- (3% +/- 1%), Br- (2% +/- 1%), Cl- (2% +/- 1%), and SO42- (3% +/- 1%) for refolding of 2 mM cyt c (anion concentration 125 mM). Dimeric cyt c obtained by refolding from the molten globule state exhibited a domain-swapped structure, in which the C-terminal alpha-helices were exchanged between protomers. According to small-angle X-ray scattering measurements, approximately 25% of the cyt c molecules were dimerized in the molten globule state containing 125 mM ClO4-. These results indicate that a certain amount of molten globule state oligomers of cyt c convert to domain-swapped oligomers during refolding and that the intermolecular interactions necessary for domain swapping are present in the molten globule state.
-
-	Formation of Domain-Swapped Oligomer of Cytochrome c from Its Molten Globule State Oligomer.,Deshpande MS, Parui PP, Kamikubo H, Yamanaka M, Nagao S, Komori H, Kataoka M, Higuchi Y, Hirota S Biochemistry. 2014 Jul 9. PMID:24981551<ref>PMID:24981551</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3wui" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deshpande~~, M S~~]]	+	[[Category: Deshpande MS]]
-	[[Category: Higuchi, Y]]	+	[[Category: Higuchi Y]]
-	[[Category: Hirota, S]]	+	[[Category: Hirota S]]
-	[[Category: Kamikubo, H]]	+	[[Category: Kamikubo H]]
-	[[Category: Kataoka, M]]	+	[[Category: Kataoka M]]
-	[[Category: Komori, H]]	+	[[Category: Komori H]]
-	[[Category: Nagao, S]]	+	[[Category: Nagao S]]
-	[[Category: Parui~~, P P~~]]	+	[[Category: Parui PP]]
-	[[Category: Yamanaka, M]]	+	[[Category: Yamanaka M]]
-	~~[[Category: Electron transport~~]]	+

OCA at 05:32, 10 August 2022

2022-08-10T05:32:03Z

←Older revision		Revision as of 05:32, 10 August 2022
Line 3:		Line 3:
	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3wui' size='340' side='right'caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WUI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wc8\|3wc8]]</div></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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [~~http~~://pdbe.org/3wui PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wui PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui 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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [https://pdbe.org/3wui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [https://www.ebi.ac.uk/pdbsum/3wui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE]] 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. Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).	+	[[https://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE]] 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. Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:47, 2 October 2019

2019-10-02T10:47:16Z

←Older revision		Revision as of 10:47, 2 October 2019
Line 1:		Line 1:

	==Dimeric horse cytochrome c formed by refolding from molten globule state==		==Dimeric horse cytochrome c formed by refolding from molten globule state==
-	<StructureSection load='3wui' size='340' side='right' caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3wui' size='340' side='right'caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUI FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUI 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>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://pdbe.org/3wui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui 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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://pdbe.org/3wui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Cytochrome c\|Cytochrome c]]	+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
		+	[[Category: Large Structures]]
	[[Category: Deshpande, M S]]		[[Category: Deshpande, M S]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]

OCA at 07:51, 4 August 2016

2016-08-04T07:51:16Z

←Older revision		Revision as of 07:51, 4 August 2016
Line 1:		Line 1:
		+
	==Dimeric horse cytochrome c formed by refolding from molten globule state==		==Dimeric horse cytochrome c formed by refolding from molten globule state==
	<StructureSection load='3wui' size='340' side='right' caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3wui' size='340' side='right' caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</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>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui 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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://pdbe.org/3wui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wui ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3wui" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c\|Cytochrome c]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:04, 25 December 2014

2014-12-25T07:04:51Z

←Older revision		Revision as of 07:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUI FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><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>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui 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=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYC_HORSE CYC_HORSE]] 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. Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
-	[[Category: Deshpande, M S.]]	+	[[Category: Deshpande, M S]]
-	[[Category: Higuchi, Y.]]	+	[[Category: Higuchi, Y]]
-	[[Category: Hirota, S.]]	+	[[Category: Hirota, S]]
-	[[Category: Kamikubo, H.]]	+	[[Category: Kamikubo, H]]
-	[[Category: Kataoka, M.]]	+	[[Category: Kataoka, M]]
-	[[Category: Komori, H.]]	+	[[Category: Komori, H]]
-	[[Category: Nagao, S.]]	+	[[Category: Nagao, S]]
-	[[Category: Parui, P P.]]	+	[[Category: Parui, P P]]
-	[[Category: Yamanaka, M.]]	+	[[Category: Yamanaka, M]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 10:22, 16 July 2014

2014-07-16T10:22:37Z

←Older revision		Revision as of 10:22, 16 July 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Dimeric horse cytochrome c formed by refolding from molten globule state==
		+	<StructureSection load='3wui' size='340' side='right' caption='[[3wui]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wui]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WUI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WUI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wc8\|3wc8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wui OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wui RCSB], [http://www.ebi.ac.uk/pdbsum/3wui PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many proteins, including cytochrome c (cyt c), have been shown to form domain-swapped oligomers, but the factors governing the oligomerization process remain unrevealed. We obtained oligomers of cyt c by refolding cyt c from its acid molten globule state to neutral pH state under high protein and ion concentrations. The amount of oligomeric cyt c obtained depended on the nature of the anion (chaotropic or kosmotropic) in the solution: ClO4- (oligomers, 11% +/- 2% (heme unit)), SCN- (10% +/- 2%), I- (6% +/- 2%), NO3- (3% +/- 1%), Br- (2% +/- 1%), Cl- (2% +/- 1%), and SO42- (3% +/- 1%) for refolding of 2 mM cyt c (anion concentration 125 mM). Dimeric cyt c obtained by refolding from the molten globule state exhibited a domain-swapped structure, in which the C-terminal alpha-helices were exchanged between protomers. According to small-angle X-ray scattering measurements, approximately 25% of the cyt c molecules were dimerized in the molten globule state containing 125 mM ClO4-. These results indicate that a certain amount of molten globule state oligomers of cyt c convert to domain-swapped oligomers during refolding and that the intermolecular interactions necessary for domain swapping are present in the molten globule state.

-	~~The entry 3wui is ON HOLD until Paper Publication~~	+	Formation of Domain-Swapped Oligomer of Cytochrome c from Its Molten Globule State Oligomer.,Deshpande MS, Parui PP, Kamikubo H, Yamanaka M, Nagao S, Komori H, Kataoka M, Higuchi Y, Hirota S Biochemistry. 2014 Jul 9. PMID:24981551<ref>PMID:24981551</ref>

-	~~Authors~~: Deshpande, M.S., ~~Parui, P.P~~., Kamikubo, H.~~, Yamanaka~~, M., Nagao, S., ~~Komori, H~~.~~, Kataoka~~, M.~~, Higuchi, Y., Hirota, S.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Dimeric horse cytochrome c formed by refolding from molten globule state~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Equus caballus]]
		+	[[Category: Deshpande, M S.]]
		+	[[Category: Higuchi, Y.]]
		+	[[Category: Hirota, S.]]
		+	[[Category: Kamikubo, H.]]
		+	[[Category: Kataoka, M.]]
		+	[[Category: Komori, H.]]
		+	[[Category: Nagao, S.]]
		+	[[Category: Parui, P P.]]
		+	[[Category: Yamanaka, M.]]
		+	[[Category: Electron transport]]

OCA at 07:00, 14 May 2014

2014-05-14T07:00:58Z

←Older revision		Revision as of 07:00, 14 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wui is ON HOLD	+	The entry 3wui is ON HOLD until Paper Publication

-	Authors: Deshpande, M. S., Parui, P.P., Kamikubo, H., Yamanaka, M., Nagao, S., Komori, H., Kataoka, M., Higuchi, Y., Hirota, S.	+	Authors: Deshpande, M.S., Parui, P.P., Kamikubo, H., Yamanaka, M., Nagao, S., Komori, H., Kataoka, M., Higuchi, Y., Hirota, S.

	Description: Dimeric horse cytochrome c formed by refolding from molten globule state		Description: Dimeric horse cytochrome c formed by refolding from molten globule state

OCA: Protected "3wui" [edit=sysop:move=sysop]

2014-04-30T05:43:25Z

Protected "3wui" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:43, 30 April 2014

OCA: New page: '''Unreleased structure''' The entry 3wui is ON HOLD Authors: Deshpande, M. S., Parui, P.P., Kamikubo, H., Yamanaka, M., Nagao, S., Komori, H., Kataoka, M., Higuchi, Y., Hirota, S. Des...

2014-04-30T05:43:23Z

New page: '''Unreleased structure''' The entry 3wui is ON HOLD Authors: Deshpande, M. S., Parui, P.P., Kamikubo, H., Yamanaka, M., Nagao, S., Komori, H., Kataoka, M., Higuchi, Y., Hirota, S. Des...

New page

'''Unreleased structure'''

The entry 3wui is ON HOLD

Authors: Deshpande, M. S., Parui, P.P., Kamikubo, H., Yamanaka, M., Nagao, S., Komori, H., Kataoka, M., Higuchi, Y., Hirota, S.

Description: Dimeric horse cytochrome c formed by refolding from molten globule state