2n2k - Revision history

OCA at 08:14, 8 March 2023

OCA — Wed, 08 Mar 2023 08:14:38 GMT

←Older revision		Revision as of 08:14, 8 March 2023
Line 1:		Line 1:

	==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==		==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==
-	<StructureSection load='2n2k' size='340' side='right'caption='[[2n2k~~]], [[NMR_Ensembles_of_Models \| 70 NMR models~~]]' scene=''>	+	<StructureSection load='2n2k' size='340' side='right'caption='[[2n2k]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ubq\|1ubq]], [[3h7p\|3h7p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [https://pdbe.org/2n2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [https://www.ebi.ac.uk/pdbsum/2n2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2k 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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [https://pdbe.org/2n2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [https://www.ebi.ac.uk/pdbsum/2n2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2k 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/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 ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gong, Z]]	+	[[Category: Gong Z]]
-	[[Category: Liu, Z]]	+	[[Category: Liu Z]]
-	[[Category: Tang, C]]	+	[[Category: Tang C]]
-	~~[[Category: Ensemble structure]]~~	+
-	~~[[Category: Polyubiquitin]]~~	+
-	~~[[Category: Protein dynamic]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Ubiquitin signaling~~]]	+

OCA at 15:25, 2 June 2021

OCA — Wed, 02 Jun 2021 15:25:52 GMT

←Older revision		Revision as of 15:25, 2 June 2021
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==		==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==
-	<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>	+	<StructureSection load='2n2k' size='340' side='right'caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2N2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ubq\|1ubq]], [[3h7p\|3h7p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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">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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [~~http~~://pdbe.org/2n2k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2n2k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2k 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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [https://pdbe.org/2n2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [https://www.ebi.ac.uk/pdbsum/2n2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2k ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== 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 ==
Line 26:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gong, Z]]		[[Category: Gong, Z]]
	[[Category: Liu, Z]]		[[Category: Liu, Z]]

OCA at 15:57, 16 November 2017

OCA — Thu, 16 Nov 2017 15:57:43 GMT

←Older revision		Revision as of 15:57, 16 November 2017
Line 1:		Line 1:
		+	{{Large structure}}
	==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==		==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==
	<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>		<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [http://pdbe.org/2n2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [http://www.ebi.ac.uk/pdbsum/2n2k PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [http://pdbe.org/2n2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [http://www.ebi.ac.uk/pdbsum/2n2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2k ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Gong, Z]]		[[Category: Gong, Z]]
	[[Category: Liu, Z]]		[[Category: Liu, Z]]

OCA at 07:31, 30 September 2015

OCA — Wed, 30 Sep 2015 07:31:45 GMT

←Older revision		Revision as of 07:31, 30 September 2015
Line 1:		Line 1:
-	==Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand==	+	==Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand==
	<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>		<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [http://www.ebi.ac.uk/pdbsum/2n2k 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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [http://pdbe.org/2n2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [http://www.ebi.ac.uk/pdbsum/2n2k PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== 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>
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2n2k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 25:
	[[Category: Gong, Z]]		[[Category: Gong, Z]]
	[[Category: Liu, Z]]		[[Category: Liu, Z]]
		+	[[Category: Tang, C]]
	[[Category: Ensemble structure]]		[[Category: Ensemble structure]]
	[[Category: Polyubiquitin]]		[[Category: Polyubiquitin]]

OCA at 14:43, 8 July 2015

OCA — Wed, 08 Jul 2015 14:43:36 GMT

←Older revision		Revision as of 14:43, 8 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand==
		+	<StructureSection load='2n2k' size='340' side='right' caption='[[2n2k]], [[NMR_Ensembles_of_Models \| 70 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2n2k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ubq\|1ubq]], [[3h7p\|3h7p]]</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=2n2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2n2k RCSB], [http://www.ebi.ac.uk/pdbsum/2n2k PDBsum]</span></td></tr>
		+	</table>
		+	== 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A polyubiquitin comprises multiple covalently linked ubiquitins and recognizes myriad targets. Free or bound to ligands, a polyubiquitin is found in different arrangements of ubiquitin subunits. To understand the structural basis for polyubiquitin quaternary plasticity and to explore the target recognition mechanism, we characterize the conformational space of Lys63-linked diubiquitin (K63-Ub2). Refining against inter-subunit paramagnetic NMR data, we show that free K63-Ub2 exists as a dynamic ensemble comprising multiple closed and open quaternary states. The quaternary dynamics enables K63-Ub2 to be specifically recognized in a variety of signaling pathways. When binding to a target protein, one of the preexisting quaternary states is selected and stabilized. A point mutation that shifts the equilibrium between the different states modulates the binding affinities towards K63-Ub2 ligands. This conformational selection mechanism at quaternary level may be used by polyubiquitins of different lengths and linkages for target recognition.

-	~~The entry 2n2k is ON HOLD until Paper Publication~~	+	Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition.,Liu Z, Gong Z, Jiang WX, Yang J, Zhu WK, Guo DC, Zhang WP, Liu ML, Tang C Elife. 2015 Jun 19;4. doi: 10.7554/eLife.05767. PMID:26090905<ref>PMID:26090905</ref>

-	~~Authors: Liu~~, Z.~~, Gong, Z~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gong, Z]]		[[Category: Gong, Z]]
	[[Category: Liu, Z]]		[[Category: Liu, Z]]
		+	[[Category: Ensemble structure]]
		+	[[Category: Polyubiquitin]]
		+	[[Category: Protein dynamic]]
		+	[[Category: Signaling protein]]
		+	[[Category: Ubiquitin signaling]]

OCA at 09:24, 17 June 2015

OCA — Wed, 17 Jun 2015 09:24:07 GMT

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	Authors: Liu, Z., Gong, Z.		Authors: Liu, Z., Gong, Z.

OCA: Protected "2n2k" [edit=sysop:move=sysop]

OCA — Wed, 20 May 2015 07:00:24 GMT

Protected "2n2k" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:00, 20 May 2015

OCA: New page: '''Unreleased structure''' The entry 2n2k is ON HOLD Authors: Liu, Z., Gong, Z. Description: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand ...

OCA — Wed, 20 May 2015 07:00:23 GMT

New page: '''Unreleased structure''' The entry 2n2k is ON HOLD Authors: Liu, Z., Gong, Z. Description: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand ...

New page

'''Unreleased structure'''

The entry 2n2k is ON HOLD

Authors: Liu, Z., Gong, Z.

Description: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand
[[Category: Unreleased Structures]]
[[Category: Gong, Z]]
[[Category: Liu, Z]]