2kde - Revision history

OCA at 08:17, 7 April 2021

2021-04-07T08:17:46Z

←Older revision		Revision as of 08:17, 7 April 2021
Line 1:		Line 1:

	==NMR structure of major S5a (196-306):K48 linked diubiquitin species==		==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
-	<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>	+	<StructureSection load='2kde' size='340' side='right'caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KDE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([~~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">PSMD4, MCB1 ([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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [~~http~~://pdbe.org/2kde PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2kde PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2kde 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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [https://pdbe.org/2kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [https://www.ebi.ac.uk/pdbsum/2kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kde ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[~~http~~://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA]] 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 (By similarity).	+	[[https://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[https://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Proteasome\|Proteasome]]	+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
-	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]	+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: African clawed frog]]		[[Category: African clawed frog]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cole, J L]]		[[Category: Cole, J L]]
	[[Category: Ehlinger, A]]		[[Category: Ehlinger, A]]

OCA at 11:15, 18 July 2018

2018-07-18T11:15:55Z

←Older revision		Revision as of 11:15, 18 July 2018
Line 1:		Line 1:
		+
	==NMR structure of major S5a (196-306):K48 linked diubiquitin species==		==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
	<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>		<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([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">PSMD4, MCB1 ([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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://pdbe.org/2kde PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde 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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://pdbe.org/2kde PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kde ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kde_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kde_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 48:		Line 49:
	[[Category: Wang, Q]]		[[Category: Wang, Q]]
	[[Category: Zhang, N]]		[[Category: Zhang, N]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Cytoplasm]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
Line 54:		Line 57:
	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: Ubiquitin interacting motif]]		[[Category: Ubiquitin interacting motif]]
		+	[[Category: Ubl conjugation]]

OCA at 19:29, 9 February 2016

2016-02-09T19:29:39Z

←Older revision		Revision as of 19:29, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2kde ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:22, 11 September 2015

2015-09-11T01:22:43Z

←Older revision		Revision as of 01:22, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>		<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Xenopus_laevis Xenopus laevis~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde 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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://pdbe.org/2kde PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[http://www.uniprot.org/uniprot/~~UBIQ_XENLA UBIQ_XENLA~~]] 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 (By similarity).	+	[[http://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[http://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 2kde" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: African clawed frog]]
-	[[Category: ~~Xenopus laevis~~]]	+	[[Category: Human]]
	[[Category: Cole, J L]]		[[Category: Cole, J L]]
	[[Category: Ehlinger, A]]		[[Category: Ehlinger, A]]

OCA at 09:02, 25 December 2014

2014-12-25T09:02:42Z

←Older revision		Revision as of 09:02, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde 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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN]] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. [[http://www.uniprot.org/uniprot/UBIQ_XENLA UBIQ_XENLA]] 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
-	[[Category: Cole, J L.]]	+	[[Category: Cole, J L]]
-	[[Category: Ehlinger, A.]]	+	[[Category: Ehlinger, A]]
-	[[Category: Fushman, D.]]	+	[[Category: Fushman, D]]
-	[[Category: Haririnia, A.]]	+	[[Category: Haririnia, A]]
-	[[Category: Kang, Y.]]	+	[[Category: Kang, Y]]
-	[[Category: Lary, J W.]]	+	[[Category: Lary, J W]]
-	[[Category: Randles, L.]]	+	[[Category: Randles, L]]
-	[[Category: Walters, K J.]]	+	[[Category: Walters, K J]]
-	[[Category: Wang, Q.]]	+	[[Category: Wang, Q]]
-	[[Category: Zhang, N.]]	+	[[Category: Zhang, N]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]

OCA at 04:18, 29 September 2014

2014-09-29T04:18:11Z

←Older revision		Revision as of 04:18, 29 September 2014
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-	[[~~Image:~~2kde.~~png~~\|~~left~~\|200px]]	+	==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
		+	<StructureSection load='2kde' size='340' side='right' caption='[[2kde]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yx4\|1yx4]], [[1yx5\|1yx5]], [[1yx6\|1yx6]], [[1d3z\|1d3z]], [[2kdf\|2kdf]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [http://www.ebi.ac.uk/pdbsum/2kde PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/2kde_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.

-	~~{{STRUCTURE_2kde\| PDB=2kde \| SCENE= }}~~	+	Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.,Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Haririnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ Mol Cell. 2009 Aug 14;35(3):280-90. PMID:19683493<ref>PMID:19683493</ref>

-	~~===NMR structure~~ of ~~major S5a (196-306):K48 linked diubiquitin species===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19683493}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2kde]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http://en~~.~~wikipedia.org~~/~~wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].~~	+

	==See Also==		==See Also==
	*[[Proteasome\|Proteasome]]		*[[Proteasome\|Proteasome]]
	*[[Ubiquitin\|Ubiquitin]]		*[[Ubiquitin\|Ubiquitin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019683493<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]

OCA at 14:53, 20 October 2012

2012-10-20T14:53:58Z

←Older revision		Revision as of 14:53, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2kde]] is a 3 chain structure ~~of [[Proteasome]] and [[Ubiquitin]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].	+	[[2kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].

	==See Also==		==See Also==

OCA at 16:37, 26 July 2012

2012-07-26T16:37:33Z

←Older revision		Revision as of 16:37, 26 July 2012
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	[[Image:2kde.png\|left\|200px]]		[[Image:2kde.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2kde", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2kde\| PDB=2kde \| SCENE= }}		{{STRUCTURE_2kde\| PDB=2kde \| SCENE= }}

	===NMR structure of major S5a (196-306):K48 linked diubiquitin species===		===NMR structure of major S5a (196-306):K48 linked diubiquitin species===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19683493}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19683493 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19683493}}		{{ABSTRACT_PUBMED_19683493}}

	==About this Structure==		==About this Structure==
-	[[2kde]] is a 3 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].	+	[[2kde]] is a 3 chain structure of [[Proteasome]] and [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].

	==See Also==		==See Also==
-	*[[Ubiquitin]]	+	*[[Proteasome\|Proteasome]]
		+	*[[Ubiquitin\|Ubiquitin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19683493~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019683493</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
Line 38:		Line 28:
	[[Category: Wang, Q.]]		[[Category: Wang, Q.]]
	[[Category: Zhang, N.]]		[[Category: Zhang, N.]]
-	[[Category: Alternative splicing]]
-	[[Category: Cytoplasm]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
Line 46:		Line 34:
	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: Ubiquitin interacting motif]]		[[Category: Ubiquitin interacting motif]]
-	[[Category: Ubl conjugation]]

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

2010-12-26T23:22:40Z

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

←Older revision

Revision as of 23:22, 26 December 2010

OCA at 23:22, 26 December 2010

2010-12-26T23:22:38Z

←Older revision		Revision as of 23:22, 26 December 2010
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-	~~{{Seed}}~~	+	[[Image:2kde.png\|left\|200px]]
-	[[Image:2kde.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	~~2KDE~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].	+	[[2kde]] is a 3 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].
		+
		+	==See Also==
		+	*[[Ubiquitin]]

	==Reference==		==Reference==
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	[[Category: Ubiquitin interacting motif]]		[[Category: Ubiquitin interacting motif]]
	[[Category: Ubl conjugation]]		[[Category: Ubl conjugation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 15:54:30 2009''