5xdo - Revision history

OCA at 08:00, 22 November 2023

OCA — Wed, 22 Nov 2023 08:00:17 GMT

←Older revision		Revision as of 08:00, 22 November 2023
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	<StructureSection load='5xdo' size='340' side='right'caption='[[5xdo]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='5xdo' size='340' side='right'caption='[[5xdo]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xdo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xdo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XDO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LNK:PENTANE'>LNK</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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]] 3.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xdn\|5xdn]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LNK:PENTANE'>LNK</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></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=5xdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdo OCA], [~~http~~://pdbe.org/5xdo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xdo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xdo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdo 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=5xdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdo OCA], [https://pdbe.org/5xdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xdo RCSB], [https://www.ebi.ac.uk/pdbsum/5xdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VDAC1_HUMAN VDAC1_HUMAN]] Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.<ref>PMID:11845315</ref> <ref>PMID:15033708</ref> <ref>PMID:18755977</ref>	+	[https://www.uniprot.org/uniprot/VDAC1_HUMAN VDAC1_HUMAN] Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.<ref>PMID:11845315</ref> <ref>PMID:15033708</ref> <ref>PMID:18755977</ref>
	<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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hosaka, T]]	+	[[Category: Hosaka T]]
-	[[Category: Kimura-Someya, T]]	+	[[Category: Kimura-Someya T]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	~~[[Category: Beta-barrel structure]]~~	+
-	~~[[Category: Cell-free synthesis]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 06:46, 14 October 2020

OCA — Wed, 14 Oct 2020 06:46:55 GMT

←Older revision		Revision as of 06:46, 14 October 2020
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	==Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group==		==Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group==
-	<StructureSection load='5xdo' size='340' side='right' caption='[[5xdo]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='5xdo' size='340' side='right'caption='[[5xdo]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xdo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xdo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XDO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LNK:PENTANE'>LNK</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LNK:PENTANE'>LNK</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xdn\|5xdn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xdn\|5xdn]]</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=5xdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdo OCA], [http://pdbe.org/5xdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdo RCSB], [http://www.ebi.ac.uk/pdbsum/5xdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdo 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=5xdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdo OCA], [http://pdbe.org/5xdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdo RCSB], [http://www.ebi.ac.uk/pdbsum/5xdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5xdo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xdo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hosaka, T]]		[[Category: Hosaka, T]]
	[[Category: Kimura-Someya, T]]		[[Category: Kimura-Someya, T]]

OCA at 03:39, 6 September 2017

OCA — Wed, 06 Sep 2017 03:39:14 GMT

←Older revision		Revision as of 03:39, 6 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xdo is ~~ON HOLD~~	+	==Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group==
		+	<StructureSection load='5xdo' size='340' side='right' caption='[[5xdo]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xdo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XDO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LNK:PENTANE'>LNK</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xdn\|5xdn]]</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=5xdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdo OCA], [http://pdbe.org/5xdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdo RCSB], [http://www.ebi.ac.uk/pdbsum/5xdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VDAC1_HUMAN VDAC1_HUMAN]] Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.<ref>PMID:11845315</ref> <ref>PMID:15033708</ref> <ref>PMID:18755977</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P221 21 , which diffracted to a resolution of 3.10 and 3.15 A, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P221 21 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with beta-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family.

-	~~Authors~~:	+	Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.,Hosaka T, Okazaki M, Kimura-Someya T, Ishizuka-Katsura Y, Ito K, Yokoyama S, Dodo K, Sodeoka M, Shirouzu M Protein Sci. 2017 Sep;26(9):1749-1758. doi: 10.1002/pro.3211. Epub 2017 Jun 21. PMID:28608415<ref>PMID:28608415</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xdo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hosaka, T]]
		+	[[Category: Kimura-Someya, T]]
		+	[[Category: Shirouzu, M]]
		+	[[Category: Beta-barrel structure]]
		+	[[Category: Cell-free synthesis]]
		+	[[Category: Membrane protein]]

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

OCA — Wed, 05 Apr 2017 12:31:44 GMT

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

←Older revision

Revision as of 12:31, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xdo is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 12:31:43 GMT

New page: '''Unreleased structure''' The entry 5xdo is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xdo is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]