6op8 - Revision history

OCA at 07:14, 11 October 2023

OCA — Wed, 11 Oct 2023 07:14:37 GMT

←Older revision		Revision as of 07:14, 11 October 2023
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	<StructureSection load='6op8' size='340' side='right'caption='[[6op8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6op8' size='340' side='right'caption='[[6op8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6op8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OP8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6op8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OP8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.703Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ubc7, ubcp3, SPBP16F5.04 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=284812 Fission yeast])~~, ~~SPCC4G3.13c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23]~~ </~~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=6op8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op8 OCA], [https://pdbe.org/6op8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6op8 RCSB], [https://www.ebi.ac.uk/pdbsum/6op8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6op8 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=6op8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op8 OCA], [~~http~~://pdbe.org/6op8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6op8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6op8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6op8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBC7_SCHPO UBC7_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the doa10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and 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) (By similarity). Together with hrd1, required for the degradation of the transcription factor sre1 precursor in the absence of its binding partner scp1. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref> <ref>PMID:19520858</ref>	+	[https://www.uniprot.org/uniprot/UBC7_SCHPO UBC7_SCHPO] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the doa10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and 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) (By similarity). Together with hrd1, required for the degradation of the transcription factor sre1 precursor in the absence of its binding partner scp1. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref> <ref>PMID:19520858</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6op8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6op8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[3D structures of ubiquitin conjugating enzyme\|3D structures of ubiquitin conjugating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: E2 ubiquitin-conjugating enzyme]]
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hann, Z S]]~~	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	~~[[Category: Lima, C D]]~~	+	[[Category: Hann ZS]]
-	~~[[Category: Endoplasmic reticulum~~-~~associated degradation~~]]	+	[[Category: Lima CD]]
-	[[Category: ~~Ligase~~]]	+
-	[[Category: ~~Ligase-protein binding complex]]~~	+
-	~~[[Category: Ubl conjugation pathway~~]]	+

OCA at 06:40, 21 August 2019

OCA — Wed, 21 Aug 2019 06:40:48 GMT

←Older revision		Revision as of 06:40, 21 August 2019
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	<StructureSection load='6op8' size='340' side='right'caption='[[6op8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6op8' size='340' side='right'caption='[[6op8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6op8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OP8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6op8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OP8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ubc7, ubcp3, SPBP16F5.04 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), SPCC4G3.13c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </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=6op8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op8 OCA], [http://pdbe.org/6op8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6op8 RCSB], [http://www.ebi.ac.uk/pdbsum/6op8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6op8 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=6op8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op8 OCA], [http://pdbe.org/6op8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6op8 RCSB], [http://www.ebi.ac.uk/pdbsum/6op8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6op8 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBC7_SCHPO UBC7_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the doa10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and 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) (By similarity). Together with hrd1, required for the degradation of the transcription factor sre1 precursor in the absence of its binding partner scp1. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref> <ref>PMID:19520858</ref>		[[http://www.uniprot.org/uniprot/UBC7_SCHPO UBC7_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the doa10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and 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) (By similarity). Together with hrd1, required for the degradation of the transcription factor sre1 precursor in the absence of its binding partner scp1. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref> <ref>PMID:19520858</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality-control pathway in eukaryotes in which misfolded ER proteins are polyubiquitylated, extracted and ultimately degraded by the proteasome. This process involves ER membrane-embedded ubiquitin E2 and E3 enzymes, as well as a soluble E2 enzyme (Ubc7 in Saccharomyces cerevisiae and UBE2G2 in mammals). E2-binding regions (E2BRs) that recruit these soluble ERAD E2s to the ER have been identified in humans and S. cerevisiae, and structures of E2-E2BR complexes from both species have been determined. In addition to sequence and structural differences between the human and S. cerevisiae E2BRs, the binding of E2BRs also elicits different biochemical outcomes with respect to E2 charging by E1 and E2 discharge. Here, the Schizosaccharomyces pombe E2BR was identified and purified with Ubc7 to resolve a 1.7 A resolution co-crystal structure of the E2BR in complex with Ubc7. The S. pombe E2BR binds to the back side of the E2 as an alpha-helix and, while differences exist, it exhibits greater similarity to the human E2BR. Structure-based sequence alignments reveal differences and conserved elements among these species. Structural comparisons and biochemistry reveal that the S. pombe E2BR presents a steric impediment to E1 binding and inhibits E1-mediated charging, respectively.
		+
		+	Crystal structure of the Schizosaccharomyces pombe U7BR E2-binding region in complex with Ubc7.,Hann ZS, Metzger MB, Weissman AM, Lima CD Acta Crystallogr F Struct Biol Commun. 2019 Aug 1;75(Pt 8):552-560. doi:, 10.1107/S2053230X19009786. Epub 2019 Aug 2. PMID:31397327<ref>PMID:31397327</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6op8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: E2 ubiquitin-conjugating enzyme]]		[[Category: E2 ubiquitin-conjugating enzyme]]
		+	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hann, Z S]]		[[Category: Hann, Z S]]

OCA at 05:59, 7 August 2019

OCA — Wed, 07 Aug 2019 05:59:08 GMT

←Older revision		Revision as of 05:59, 7 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6op8 is ~~ON HOLD until Paper Publication~~	+	==S. pombe Ubc7/U7BR complex==
-		+	<StructureSection load='6op8' size='340' side='right'caption='[[6op8]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6op8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OP8 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E2_ubiquitin-conjugating_enzyme E2 ubiquitin-conjugating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.23 2.3.2.23] </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=6op8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op8 OCA], [http://pdbe.org/6op8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6op8 RCSB], [http://www.ebi.ac.uk/pdbsum/6op8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6op8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC7_SCHPO UBC7_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. Cognate E2 conjugating enzyme for the doa10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains, and 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) (By similarity). Together with hrd1, required for the degradation of the transcription factor sre1 precursor in the absence of its binding partner scp1. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref> <ref>PMID:19520858</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: E2 ubiquitin-conjugating enzyme]]
		+	[[Category: Large Structures]]
		+	[[Category: Hann, Z S]]
		+	[[Category: Lima, C D]]
		+	[[Category: Endoplasmic reticulum-associated degradation]]
		+	[[Category: Ligase]]
		+	[[Category: Ligase-protein binding complex]]
		+	[[Category: Ubl conjugation pathway]]

OCA at 07:54, 10 May 2019

OCA — Fri, 10 May 2019 07:54:16 GMT

←Older revision		Revision as of 07:54, 10 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6op8 is ON HOLD	+	The entry 6op8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6op8" [edit=sysop:move=sysop]

OCA — Wed, 01 May 2019 07:16:44 GMT

Protected "6op8" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:16, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6op8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 May 2019 07:16:43 GMT

New page: '''Unreleased structure''' The entry 6op8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6op8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]