4ksj - Revision history

OCA at 09:11, 7 December 2022

2022-12-07T09:11:15Z

←Older revision		Revision as of 09:11, 7 December 2022
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	==Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom==		==Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom==
-	<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4ksj' size='340' side='right'caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ksj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KSJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KSJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ksj]] is a 1 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=4KSJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KSJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [https://pdbe.org/4ksj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [https://www.ebi.ac.uk/pdbsum/4ksj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ksj ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FAM105B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [~~http~~://pdbe.org/4ksj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ksj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ksj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/OTUL_HUMAN OTUL_HUMAN] Deubiquitinase that specifically removes linear ('Met-1'-linked) polyubiquitin chains to substrates and acts as a regulator of angiogenesis and innate immune response. Associates with the LUBAC complex via direct interaction with RNF31 and counteracts its action by cleaving linear polyubiquitin chains to substrates. Required during angiogenesis, craniofacial and neuronal development by regulating the canonical Wnt signaling together with the LUBAC complex. Acts as a negative regulator of NF-kappa-B by counteracting activity of the LUBAC complex. Plays a key role in innate immune response: required to restrict linear polyubiquitin formation on RIPK2 in response to NOD2 stimulation, probably to limit NOD2-dependent proinflammatory signaling.<ref>PMID:23827681</ref> <ref>PMID:23806334</ref> <ref>PMID:23746843</ref> <ref>PMID:23708998</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Ceccarelli, D F~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Juang, Y C~~]]	+	[[Category: Ceccarelli DF]]
-	[[Category: ~~Sicheri, F~~]]	+	[[Category: Juang Y-C]]
-	[[Category: ~~Deubiquitinase]]~~	+	[[Category: Sicheri F]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Otu domain]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 06:08, 18 April 2018

2018-04-18T06:08:24Z

←Older revision		Revision as of 06:08, 18 April 2018
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	<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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://pdbe.org/4ksj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ksj 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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://pdbe.org/4ksj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ksj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A complex interaction of signalling events, including the Wnt pathway, regulates sprouting of blood vessels from pre-existing vasculature during angiogenesis. Here we show that two distinct mutations in the (uro)chordate-specific gumby (also called Fam105b) gene cause an embryonic angiogenic phenotype in gumby mice. Gumby interacts with disheveled 2 (DVL2), is expressed in canonical Wnt-responsive endothelial cells and encodes an ovarian tumour domain class of deubiquitinase that specifically cleaves linear ubiquitin linkages. A crystal structure of gumby in complex with linear diubiquitin reveals how the identified mutations adversely affect substrate binding and catalytic function in line with the severity of their angiogenic phenotypes. Gumby interacts with HOIP (also called RNF31), a key component of the linear ubiquitin assembly complex, and decreases linear ubiquitination and activation of NF-kappaB-dependent transcription. This work provides support for the biological importance of linear (de)ubiquitination in angiogenesis, craniofacial and neural development and in modulating Wnt signalling.
		+
		+	The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.,Rivkin E, Almeida SM, Ceccarelli DF, Juang YC, MacLean TA, Srikumar T, Huang H, Dunham WH, Fukumura R, Xie G, Gondo Y, Raught B, Gingras AC, Sicheri F, Cordes SP Nature. 2013 Jun 20;498(7454):318-24. doi: 10.1038/nature12296. Epub 2013 May 24. PMID:23708998<ref>PMID:23708998</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ksj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:12, 11 August 2016

2016-08-11T10:12:00Z

←Older revision		Revision as of 10:12, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom==		==Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom==
	<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FAM105B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FAM105B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj 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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://pdbe.org/4ksj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ksj ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 11:03, 25 January 2015

2015-01-25T11:03:55Z

←Older revision		Revision as of 11:03, 25 January 2015
Line 2:		Line 2:
	<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ksj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KSJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ksj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KSJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FAM105B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj 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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj PDBsum]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Ceccarelli, D F]]		[[Category: Ceccarelli, D F]]
	[[Category: Juang, Y C]]		[[Category: Juang, Y C]]

OCA at 07:37, 12 November 2014

2014-11-12T07:37:31Z

←Older revision		Revision as of 07:37, 12 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ksj\| PDB=4ksj \| SCENE= }}~~	+	==Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom==
-	===Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom===	+	<StructureSection load='4ksj' size='340' side='right' caption='[[4ksj]], [[Resolution\|resolution]] 1.60Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4ksj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KSJ FirstGlance]. <br>
-	[[4ksj]] is a 1 chain structure ~~with sequence~~ from [http://en.~~wikipedia~~.~~org~~/~~wiki~~/~~Homo_sapiens Homo sapiens~~]. ~~Full crystallographic information is available from~~ [http://oca.weizmann.ac.il/oca-~~bin~~/~~ocashort~~?id=4KSJ ~~OCA~~].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[~~Category~~: ~~Homo sapiens~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: Ceccarelli, D F.]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ksk\|4ksk]], [[4ksl\|4ksl]]</td></tr>
-	[[Category: Juang, Y-C.]]	+	<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=4ksj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ksj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ksj RCSB], [http://www.ebi.ac.uk/pdbsum/4ksj PDBsum]</span></td></tr>
-	[[Category: Sicheri, F.]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ceccarelli, D F]]
		+	[[Category: Juang, Y C]]
		+	[[Category: Sicheri, F]]
	[[Category: Deubiquitinase]]		[[Category: Deubiquitinase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Otu domain]]		[[Category: Otu domain]]
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]

OCA: Protected "4ksj" [edit=sysop:move=sysop]

2013-06-19T18:16:56Z

Protected "4ksj" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:16, 19 June 2013

OCA: New page: {{STRUCTURE_4ksj| PDB=4ksj | SCENE= }} ===Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom=== ==About this Structure== 4ksj is a 1 chain structure with sequen...

2013-06-19T18:16:54Z

New page: {{STRUCTURE_4ksj| PDB=4ksj | SCENE= }} ===Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom=== ==About this Structure== 4ksj is a 1 chain structure with sequen...

New page

{{STRUCTURE_4ksj| PDB=4ksj | SCENE= }}
===Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom===

==About this Structure==
[[4ksj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KSJ OCA].
[[Category: Homo sapiens]]
[[Category: Ceccarelli, D F.]]
[[Category: Juang, Y-C.]]
[[Category: Sicheri, F.]]
[[Category: Deubiquitinase]]
[[Category: Hydrolase]]
[[Category: Otu domain]]
[[Category: Ubiquitin]]