3wxf - Revision history

OCA at 13:32, 8 November 2023

OCA — Wed, 08 Nov 2023 13:32:49 GMT

←Older revision		Revision as of 13:32, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3wxf' size='340' side='right'caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wxf' size='340' side='right'caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio] and [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WXF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WXF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3wxe\|3wxe]]~~, [[~~3wxg~~\|~~3wxg~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cyld, cylda ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=7955 Brachidanio rerio]), UBC ([https~~:/~~/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'>[https://proteopedia.org/fgij/fg.htm?mol=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [https://pdbe.org/3wxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [https://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf 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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [https://pdbe.org/3wxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [https://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~UBC_HUMAN UBC_HUMAN~~]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[https://www.uniprot.org/uniprot/E7FEV5_DANRE E7FEV5_DANRE]
	<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: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukai, S]]	+	[[Category: Fukai S]]
-	[[Category: Sato, Y]]	+	[[Category: Sato Y]]
-	~~[[Category: Hydrolase-protein binding complex]]~~	+
-	~~[[Category: Ubiquitin protease~~]]	+

OCA at 05:34, 10 August 2022

OCA — Wed, 10 Aug 2022 05:34:43 GMT

←Older revision		Revision as of 05:34, 10 August 2022
Line 3:		Line 3:
	<StructureSection load='3wxf' size='340' side='right'caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wxf' size='340' side='right'caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WXF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WXF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wxe\|3wxe]], [[3wxg\|3wxg]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cyld, cylda ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), UBC ([~~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">cyld, cylda ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), UBC ([https://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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [~~http~~://pdbe.org/3wxf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf 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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [https://pdbe.org/3wxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [https://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>	+	[[https://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:36, 1 January 2020

OCA — Wed, 01 Jan 2020 08:36:41 GMT

←Older revision		Revision as of 08:36, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin==		==Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin==
-	<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3wxf' size='340' side='right'caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WXF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WXF FirstGlance]. <br>
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>		[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.
		+
		+	Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.,Sato Y, Goto E, Shibata Y, Kubota Y, Yamagata A, Goto-Ito S, Kubota K, Inoue J, Takekawa M, Tokunaga F, Fukai S Nat Struct Mol Biol. 2015 Mar;22(3):222-9. doi: 10.1038/nsmb.2970. Epub 2015 Feb , 16. PMID:25686088<ref>PMID:25686088</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3wxf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 17:		Line 26:
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Sato, Y]]		[[Category: Sato, Y]]
	[[Category: Hydrolase-protein binding complex]]		[[Category: Hydrolase-protein binding complex]]
	[[Category: Ubiquitin protease]]		[[Category: Ubiquitin protease]]

OCA at 00:55, 16 November 2017

OCA — Thu, 16 Nov 2017 00:55:40 GMT

←Older revision		Revision as of 00:55, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WXF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WXF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cyld, cylda ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), UBC ([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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [http://pdbe.org/3wxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [http://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf 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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [http://pdbe.org/3wxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [http://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf ProSAT]</span></td></tr>
	</table>		</table>
Line 14:		Line 15:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
		+	[[Category: Human]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Sato, Y]]		[[Category: Sato, Y]]
	[[Category: Hydrolase-protein binding complex]]		[[Category: Hydrolase-protein binding complex]]
	[[Category: Ubiquitin protease]]		[[Category: Ubiquitin protease]]

OCA at 19:11, 10 December 2016

OCA — Sat, 10 Dec 2016 19:11:13 GMT

←Older revision		Revision as of 19:11, 10 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin==		==Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin==
	<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [http://www.ebi.ac.uk/pdbsum/3wxf 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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [http://pdbe.org/3wxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [http://www.ebi.ac.uk/pdbsum/3wxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wxf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:56, 12 February 2015

OCA — Thu, 12 Feb 2015 11:56:17 GMT

←Older revision		Revision as of 11:56, 12 February 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin==
-		+	<StructureSection load='3wxf' size='340' side='right' caption='[[3wxf]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~The entry~~ 3wxf is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3wxf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WXF FirstGlance]. <br>
-	~~Authors~~: ~~Sato~~, Y., ~~Fukai~~, S.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wxe\|3wxe]], [[3wxg\|3wxg]]</td></tr>
-	~~Description~~: ~~Crystal structure~~ of the ubiquitin ~~protease~~ in the M1-~~catalyltic state~~	+	<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=3wxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wxf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wxf RCSB], [http://www.ebi.ac.uk/pdbsum/3wxf PDBsum]</span></td></tr>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</table>
-	~~[[Category~~: ~~Sato, Y]]~~	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBC_HUMAN UBC_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
		+	[[Category: Sato, Y]]
		+	[[Category: Hydrolase-protein binding complex]]
		+	[[Category: Ubiquitin protease]]

OCA at 13:04, 24 December 2014

OCA — Wed, 24 Dec 2014 13:04:31 GMT

←Older revision		Revision as of 13:04, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of the ubiquitin protease in the M1-catalyltic state		Description: Crystal structure of the ubiquitin protease in the M1-catalyltic state
		+	[[Category: Unreleased Structures]]
		+	[[Category: Sato, Y]]
		+	[[Category: Fukai, S]]

OCA at 07:01, 13 August 2014

OCA — Wed, 13 Aug 2014 07:01:52 GMT

←Older revision		Revision as of 07:01, 13 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Sato, Y, Fukai, S	+	Authors: Sato, Y., Fukai, S.

-	Description: Crystal structure of the ubiquitin protease	+	Description: Crystal structure of the ubiquitin protease in the M1-catalyltic state

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

OCA — Thu, 07 Aug 2014 00:37:17 GMT

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

←Older revision

Revision as of 00:37, 7 August 2014

OCA: New page: '''Unreleased structure''' The entry 3wxf is ON HOLD Authors: Sato, Y, Fukai, S Description: Crystal structure of the ubiquitin protease

OCA — Thu, 07 Aug 2014 00:37:15 GMT

New page: '''Unreleased structure''' The entry 3wxf is ON HOLD Authors: Sato, Y, Fukai, S Description: Crystal structure of the ubiquitin protease

New page

'''Unreleased structure'''

The entry 3wxf is ON HOLD

Authors: Sato, Y, Fukai, S

Description: Crystal structure of the ubiquitin protease