5v7v - Revision history

OCA at 22:01, 10 April 2020

OCA — Fri, 10 Apr 2020 22:01:41 GMT

←Older revision		Revision as of 22:01, 10 April 2020
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	<SX load='5v7v' size='340' side='right' viewer='molstar' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>		<SX load='5v7v' size='340' side='right' viewer='molstar' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5V7V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v6p\|5v6p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v6p\|5v6p]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HRD3, YLR207W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HRD3, YLR207W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5v7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7v OCA], [http://pdbe.org/5v7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7v RCSB], [http://www.ebi.ac.uk/pdbsum/5v7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7v 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=5v7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7v OCA], [http://pdbe.org/5v7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7v RCSB], [http://www.ebi.ac.uk/pdbsum/5v7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:49, 6 March 2020

OCA — Fri, 06 Mar 2020 19:49:10 GMT

←Older revision		Revision as of 19:49, 6 March 2020
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	==Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3==		==Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3==
-	<~~StructureSection~~ load='5v7v' size='340' side='right'caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>	+	<SX load='5v7v' size='340' side='right' viewer='molstar' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:29, 1 January 2020

OCA — Wed, 01 Jan 2020 09:29:44 GMT

←Older revision		Revision as of 09:29, 1 January 2020
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	==Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3==		==Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3==
-	<StructureSection load='5v7v' size='340' side='right' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>	+	<StructureSection load='5v7v' size='340' side='right'caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Liao, M]]		[[Category: Liao, M]]
	[[Category: Mi, W]]		[[Category: Mi, W]]

OCA at 23:29, 15 November 2017

OCA — Wed, 15 Nov 2017 23:29:22 GMT

←Older revision		Revision as of 23:29, 15 November 2017
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	<StructureSection load='5v7v' size='340' side='right' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>		<StructureSection load='5v7v' size='340' side='right' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v6p\|5v6p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v6p\|5v6p]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HRD3, YLR207W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5v7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7v OCA], [http://pdbe.org/5v7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7v RCSB], [http://www.ebi.ac.uk/pdbsum/5v7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7v 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=5v7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7v OCA], [http://pdbe.org/5v7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7v RCSB], [http://www.ebi.ac.uk/pdbsum/5v7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7v ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Liao, M]]		[[Category: Liao, M]]
	[[Category: Mi, W]]		[[Category: Mi, W]]

OCA at 11:07, 24 August 2017

OCA — Thu, 24 Aug 2017 11:07:54 GMT

←Older revision		Revision as of 11:07, 24 August 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5v7v is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3==
		+	<StructureSection load='5v7v' size='340' side='right' caption='[[5v7v]], [[Resolution\|resolution]] 3.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v7v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v6p\|5v6p]]</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=5v7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7v OCA], [http://pdbe.org/5v7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7v RCSB], [http://www.ebi.ac.uk/pdbsum/5v7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7v ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HRD3_YEAST HRD3_YEAST]] Component of the endoplasmic reticulum quality control (ERQC) system involved in ubiquitin-dependent degradation of missfolded endoplasmic reticulum proteins. Component of the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). ERAD-L substrates are ubiquitinated through HRD1 in conjunction with the E2 ubiquitin-conjugating enzymes UBC1 and UBC7-CUE1. Ubiquitinated substrates are then removed to the cytosol via the action of the UFD1-NPL4-CDC48/p97 (UNC) AAA ATPase complex and targeted to the proteasome. ERAD-M substrates are processed by the same HRD1-HRD3 core complex, but only a subset of the other components is required for ERAD-M. Stabilizes the HRD1 ubiquitin-protein ligase. Has also a function in recruiting misfolded protein substrates.<ref>PMID:10218484</ref> <ref>PMID:10547371</ref> <ref>PMID:10793145</ref> <ref>PMID:11018054</ref> <ref>PMID:11390656</ref> <ref>PMID:16619026</ref> <ref>PMID:16845381</ref> <ref>PMID:16873065</ref> <ref>PMID:16873066</ref> <ref>PMID:8970163</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Misfolded endoplasmic reticulum proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the membrane, and degraded by the proteasome-a pathway termed endoplasmic reticulum-associated protein degradation (ERAD). Proteins with misfolded domains in the endoplasmic reticulum lumen or membrane are discarded through the ERAD-L and ERAD-M pathways, respectively. In Saccharomyces cerevisiae, both pathways require the ubiquitin ligase Hrd1, a multi-spanning membrane protein with a cytosolic RING finger domain. Hrd1 is the crucial membrane component for retro-translocation, but it is unclear whether it forms a protein-conducting channel. Here we present a cryo-electron microscopy structure of S. cerevisiae Hrd1 in complex with its endoplasmic reticulum luminal binding partner, Hrd3. Hrd1 forms a dimer within the membrane with one or two Hrd3 molecules associated at its luminal side. Each Hrd1 molecule has eight transmembrane segments, five of which form an aqueous cavity extending from the cytosol almost to the endoplasmic reticulum lumen, while a segment of the neighbouring Hrd1 molecule forms a lateral seal. The aqueous cavity and lateral gate are reminiscent of features of protein-conducting conduits that facilitate polypeptide movement in the opposite direction-from the cytosol into or across membranes. Our results suggest that Hrd1 forms a retro-translocation channel for the movement of misfolded polypeptides through the endoplasmic reticulum membrane.

-	~~Authors~~:	+	Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.,Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6. PMID:28682307<ref>PMID:28682307</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v7v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Liao, M]]
		+	[[Category: Mi, W]]
		+	[[Category: Rapoport, T A]]
		+	[[Category: Schoebel, S]]
		+	[[Category: Stein, A]]
		+	[[Category: Hrd3 erad]]
		+	[[Category: Protein transport]]

OCA at 13:38, 17 May 2017

OCA — Wed, 17 May 2017 13:38:43 GMT

←Older revision		Revision as of 13:38, 17 May 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v7v is ON HOLD	+	The entry 5v7v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v7v" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:42:25 GMT

Protected "5v7v" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:42, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v7v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 11:42:24 GMT

New page: '''Unreleased structure''' The entry 5v7v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v7v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]