1dv0 - Revision history

OCA at 08:25, 22 May 2024

OCA — Wed, 22 May 2024 08:25:20 GMT

←Older revision		Revision as of 08:25, 22 May 2024
Line 19:		Line 19:
	</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=1dv0 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=1dv0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DNA repair protein HHR23A is a highly conserved protein that functions in nucleotide excision repair. HHR23A contains two ubiquitin associated domains (UBA) that are conserved in a number of proteins with diverse functions involved in ubiquitination, UV excision repair, and signaling pathways via protein kinases. The cellular binding partners of UBA domains remain unclear; however, we previously found that the HHR23A UBA(2) domain interacts specifically with the HIV-1 Vpr protein. Analysis of the low resolution solution structure of HHR23A UBA(2) revealed a hydrophobic loop region of the UBA(2) domain that we predicted was the interface for protein/protein interactions. Here we present results of in vitro binding studies that demonstrate the requirement of this hydrophobic loop region for interaction with human immunodeficiency virus (HIV-1) Vpr. A single point mutation of the Pro at residue 333 to a Glu totally abolishes the binding of HIV-1 Vpr to UBA(2). High resolution NMR structures of the binding deficient UBA(2) mutant P333E as well as of the wild-type UBA(2) domain were determined to compare the effect of this mutation on the structure. Small but significant differences are observed only locally at the site of the mutation. The biochemical and structural analysis confirms the function of the HHR23A UBA(2) GFP-loop as the protein/protein interacting domain.
		+
		+	Biochemical and structural analysis of the interaction between the UBA(2) domain of the DNA repair protein HHR23A and HIV-1 Vpr.,Withers-Ward ES, Mueller TD, Chen IS, Feigon J Biochemistry. 2000 Nov 21;39(46):14103-12. PMID:11087358<ref>PMID:11087358</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1dv0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:54, 20 March 2024

OCA — Wed, 20 Mar 2024 09:54:12 GMT

←Older revision		Revision as of 09:54, 20 March 2024
Line 1:		Line 1:

	==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==		==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==
-	<StructureSection load='1dv0' size='340' side='right'caption='[[1dv0~~]], [[NMR_Ensembles_of_Models \| 18 NMR models~~]]' scene=''>	+	<StructureSection load='1dv0' size='340' side='right'caption='[[1dv0]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[1uba\|1uba]]</div~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [https://pdbe.org/1dv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [https://pdbe.org/1dv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>	+	[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</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=1dv0 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=1dv0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The DNA repair protein HHR23A is a highly conserved protein that functions in nucleotide excision repair. HHR23A contains two ubiquitin associated domains (UBA) that are conserved in a number of proteins with diverse functions involved in ubiquitination, UV excision repair, and signaling pathways via protein kinases. The cellular binding partners of UBA domains remain unclear; however, we previously found that the HHR23A UBA(2) domain interacts specifically with the HIV-1 Vpr protein. Analysis of the low resolution solution structure of HHR23A UBA(2) revealed a hydrophobic loop region of the UBA(2) domain that we predicted was the interface for protein/protein interactions. Here we present results of in vitro binding studies that demonstrate the requirement of this hydrophobic loop region for interaction with human immunodeficiency virus (HIV-1) Vpr. A single point mutation of the Pro at residue 333 to a Glu totally abolishes the binding of HIV-1 Vpr to UBA(2). High resolution NMR structures of the binding deficient UBA(2) mutant P333E as well as of the wild-type UBA(2) domain were determined to compare the effect of this mutation on the structure. Small but significant differences are observed only locally at the site of the mutation. The biochemical and structural analysis confirms the function of the HHR23A UBA(2) GFP-loop as the protein/protein interacting domain.
-
-	Biochemical and structural analysis of the interaction between the UBA(2) domain of the DNA repair protein HHR23A and HIV-1 Vpr.,Withers-Ward ES, Mueller TD, Chen IS, Feigon J Biochemistry. 2000 Nov 21;39(46):14103-12. PMID:11087358<ref>PMID:11087358</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dv0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, I S~~]]	+	[[Category: Chen IS]]
-	[[Category: Feigon, J]]	+	[[Category: Feigon J]]
-	[[Category: Mueller~~, T D~~]]	+	[[Category: Mueller TD]]
-	[[Category: Withers-Ward~~, E S]]~~	+	[[Category: Withers-Ward ES]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Helical bundle~~]]	+

OCA at 09:31, 21 July 2021

OCA — Wed, 21 Jul 2021 09:31:44 GMT

←Older revision		Revision as of 09:31, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1dv0' size='340' side='right'caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>		<StructureSection load='1dv0' size='340' side='right'caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</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;'>[[1uba\|1uba]]</div></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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [~~http~~://pdbe.org/1dv0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dv0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [https://pdbe.org/1dv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>	+	[[https://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:47, 16 October 2019

OCA — Wed, 16 Oct 2019 10:47:06 GMT

←Older revision		Revision as of 10:47, 16 October 2019
Line 1:		Line 1:

	==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==		==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==
-	<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>	+	<StructureSection load='1dv0' size='340' side='right'caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chen, I S]]		[[Category: Chen, I S]]
	[[Category: Feigon, J]]		[[Category: Feigon, J]]

OCA at 08:00, 13 December 2017

OCA — Wed, 13 Dec 2017 08:00:44 GMT

←Older revision		Revision as of 08:00, 13 December 2017
Line 1:		Line 1:
		+
	==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==		==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==
	<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>		<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://pdbe.org/1dv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://pdbe.org/1dv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv0_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>

OCA at 04:08, 8 February 2016

OCA — Mon, 08 Feb 2016 04:08:18 GMT

←Older revision		Revision as of 04:08, 8 February 2016
Line 16:		Line 16:
	<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=1dv0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:42, 10 September 2015

OCA — Thu, 10 Sep 2015 07:42:31 GMT

←Older revision		Revision as of 07:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>		<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://pdbe.org/1dv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1dv0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Chen, I S]]		[[Category: Chen, I S]]
	[[Category: Feigon, J]]		[[Category: Feigon, J]]

OCA at 20:30, 24 December 2014

OCA — Wed, 24 Dec 2014 20:30:27 GMT

←Older revision		Revision as of 20:30, 24 December 2014
Line 6:		Line 6:
	<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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (GG-NER) by association with XPC. In vitro, the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 vpr with the host proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:48, 22 December 2014

OCA — Mon, 22 Dec 2014 22:48:11 GMT

←Older revision		Revision as of 22:48, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Chen, I S.]]	+	[[Category: Chen, I S]]
-	[[Category: Feigon, J.]]	+	[[Category: Feigon, J]]
-	[[Category: Mueller, T D.]]	+	[[Category: Mueller, T D]]
-	[[Category: Withers-Ward, E S.]]	+	[[Category: Withers-Ward, E S]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Helical bundle]]		[[Category: Helical bundle]]

OCA at 04:12, 3 October 2014

OCA — Fri, 03 Oct 2014 04:12:21 GMT

←Older revision		Revision as of 04:12, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1dv0\| PDB=1dv0 \| SCENE= }}~~	+	==Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)==
-	===Refined NMR solution structure of the C-terminal UBA domain of the human homologue of RAD23A (HHR23A)===	+	<StructureSection load='1dv0' size='340' side='right' caption='[[1dv0]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_11087358}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dv0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uba\|1uba]]</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=1dv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv0 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/dv/1dv0_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 ==
		+	The DNA repair protein HHR23A is a highly conserved protein that functions in nucleotide excision repair. HHR23A contains two ubiquitin associated domains (UBA) that are conserved in a number of proteins with diverse functions involved in ubiquitination, UV excision repair, and signaling pathways via protein kinases. The cellular binding partners of UBA domains remain unclear; however, we previously found that the HHR23A UBA(2) domain interacts specifically with the HIV-1 Vpr protein. Analysis of the low resolution solution structure of HHR23A UBA(2) revealed a hydrophobic loop region of the UBA(2) domain that we predicted was the interface for protein/protein interactions. Here we present results of in vitro binding studies that demonstrate the requirement of this hydrophobic loop region for interaction with human immunodeficiency virus (HIV-1) Vpr. A single point mutation of the Pro at residue 333 to a Glu totally abolishes the binding of HIV-1 Vpr to UBA(2). High resolution NMR structures of the binding deficient UBA(2) mutant P333E as well as of the wild-type UBA(2) domain were determined to compare the effect of this mutation on the structure. Small but significant differences are observed only locally at the site of the mutation. The biochemical and structural analysis confirms the function of the HHR23A UBA(2) GFP-loop as the protein/protein interacting domain.

-	~~==Function==~~	+	Biochemical and structural analysis of the interaction between the UBA(2) domain of the DNA repair protein HHR23A and HIV-1 Vpr.,Withers-Ward ES, Mueller TD, Chen IS, Feigon J Biochemistry. 2000 Nov 21;39(46):14103-12. PMID:11087358<ref>PMID:11087358</ref>
-	~~[[http://www.uniprot.org/uniprot/RD23A_HUMAN RD23A_HUMAN]] Multiubiquitin chain receptor involved in modulation~~ of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the ~~26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to~~ the proteasome.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in nucleotide excision repair and is thought to be functional equivalent for RAD23B in global genome nucleotide excision repair (~~GG-NER~~) ~~by association with XPC. In vitro,~~ the XPC:RAD23A dimer has NER activity. Can stabilize XPC.<ref>PMID:9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref> <ref>PMID:20614012</ref> Involved in vpr-dependent replication of HIV-1 ~~in non~~-~~proliferating cells and primary macrophages~~. ~~Required for the association of HIV~~-~~1 vpr with the host proteasome~~.~~<ref>~~PMID:~~9372924</ref> <ref>PMID:14621999</ref> <ref>PMID:12643283</ref> <ref>PMID:15321727</ref>~~ <ref>PMID:~~20614012~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1dv0]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1uba 1uba]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV0 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:011087358</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chen, I S.]]		[[Category: Chen, I S.]]