1nj3 - Revision history

OCA at 08:50, 10 April 2024

OCA — Wed, 10 Apr 2024 08:50:23 GMT

←Older revision		Revision as of 08:50, 10 April 2024
Line 1:		Line 1:

	==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==		==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==
-	<StructureSection load='1nj3' size='340' side='right'caption='[[1nj3~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1nj3' size='340' side='right'caption='[[1nj3]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1fhh\|1fhh]], [[1dvb\|1dvb]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [https://pdbe.org/1nj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [https://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [~~http~~://pdbe.org/1nj3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NPL4_RAT NPL4_RAT]] The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope.<ref>PMID:10811609</ref> <ref>PMID:11781570</ref> <ref>PMID:11740563</ref> <ref>PMID:14636562</ref> <ref>PMID:12411482</ref> <ref>PMID:12644454</ref>	+	[https://www.uniprot.org/uniprot/NPL4_RAT NPL4_RAT] The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope.<ref>PMID:10811609</ref> <ref>PMID:11781570</ref> <ref>PMID:11740563</ref> <ref>PMID:14636562</ref> <ref>PMID:12411482</ref> <ref>PMID:12644454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1nj3 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=1nj3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ubiquitylated proteins are directed into a large number of different cellular pathways through interactions with effector proteins that contain conserved ubiquitin binding motifs. Here, we report the solution structure and ubiquitin binding properties of one such motif, the Npl4 zinc finger or RanBP2/Nup358 zinc finger (NZF) domain. Npl4 NZF forms a compact module composed of four antiparallel beta-strands linked by three ordered loops. A single zinc ion is coordinated by four conserved cysteines from the first and third loops, which form two rubredoxin knuckles. Npl4 NZF binds specifically, but weakly, to free ubiquitin using a conserved 13TF14 dipeptide to interact with the "Ile-44" surface of ubiquitin. Our studies reveal the structure of this versatile class of protein binding domains and provide a means for identifying the subset of NZF domains likely to bind ubiquitin.
-
-	Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.,Wang B, Alam SL, Meyer HH, Payne M, Stemmler TL, Davis DR, Sundquist WI J Biol Chem. 2003 May 30;278(22):20225-34. Epub 2003 Mar 18. PMID:12644454<ref>PMID:12644454</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nj3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Alam~~, S L~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Davis~~, D R~~]]	+	[[Category: Alam SL]]
-	[[Category: Meyer~~, H H~~]]	+	[[Category: Davis DR]]
-	[[Category: Payne, M]]	+	[[Category: Meyer HH]]
-	[[Category: Stemmler~~, T L~~]]	+	[[Category: Payne M]]
-	[[Category: Sundquist~~, W I~~]]	+	[[Category: Stemmler TL]]
-	[[Category: Wang, B]]	+	[[Category: Sundquist WI]]
-	~~[[Category: Beta-ribbon]]~~	+	[[Category: Wang B]]
-	~~[[Category: Npl4]]~~	+
-	~~[[Category: Nzf domain]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Rubredoxin knuckle]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 08:51, 2 December 2020

OCA — Wed, 02 Dec 2020 08:51:20 GMT

←Older revision		Revision as of 08:51, 2 December 2020
Line 1:		Line 1:

	==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==		==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==
-	<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1nj3' size='340' side='right'caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fhh\|1fhh]], [[1dvb\|1dvb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fhh\|1fhh]], [[1dvb\|1dvb]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1nj3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1nj3_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Alam, S L]]		[[Category: Alam, S L]]
	[[Category: Davis, D R]]		[[Category: Davis, D R]]

OCA at 07:51, 22 November 2017

OCA — Wed, 22 Nov 2017 07:51:17 GMT

←Older revision		Revision as of 07:51, 22 November 2017
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fhh\|1fhh]], [[1dvb\|1dvb]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>

OCA at 09:51, 1 November 2017

OCA — Wed, 01 Nov 2017 09:51:38 GMT

←Older revision		Revision as of 09:51, 1 November 2017
Line 1:		Line 1:
		+
	==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==		==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==
	<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nj3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=1nj3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:36, 11 September 2015

OCA — Fri, 11 Sep 2015 16:36:20 GMT

←Older revision		Revision as of 16:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://pdbe.org/1nj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1nj3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Alam, S L]]		[[Category: Alam, S L]]
	[[Category: Davis, D R]]		[[Category: Davis, D R]]

OCA at 19:05, 25 December 2014

OCA — Thu, 25 Dec 2014 19:05:21 GMT

←Older revision		Revision as of 19:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NPL4_RAT NPL4_RAT]] The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope.<ref>PMID:10811609</ref> <ref>PMID:11781570</ref> <ref>PMID:11740563</ref> <ref>PMID:14636562</ref> <ref>PMID:12411482</ref> <ref>PMID:12644454</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Alam, S L.]]	+	[[Category: Alam, S L]]
-	[[Category: Davis, D R.]]	+	[[Category: Davis, D R]]
-	[[Category: Meyer, H H.]]	+	[[Category: Meyer, H H]]
-	[[Category: Payne, M.]]	+	[[Category: Payne, M]]
-	[[Category: Stemmler, T L.]]	+	[[Category: Stemmler, T L]]
-	[[Category: Sundquist, W I.]]	+	[[Category: Sundquist, W I]]
-	[[Category: Wang, B.]]	+	[[Category: Wang, B]]
	[[Category: Beta-ribbon]]		[[Category: Beta-ribbon]]
	[[Category: Npl4]]		[[Category: Npl4]]

OCA at 13:07, 28 September 2014

OCA — Sun, 28 Sep 2014 13:07:34 GMT

←Older revision		Revision as of 13:07, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1nj3.~~png~~\|~~left~~\|200px]]	+	==Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4==
		+	<StructureSection load='1nj3' size='340' side='right' caption='[[1nj3]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJ3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Npl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=1nj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1nj3 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/nj/1nj3_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 ==
		+	Ubiquitylated proteins are directed into a large number of different cellular pathways through interactions with effector proteins that contain conserved ubiquitin binding motifs. Here, we report the solution structure and ubiquitin binding properties of one such motif, the Npl4 zinc finger or RanBP2/Nup358 zinc finger (NZF) domain. Npl4 NZF forms a compact module composed of four antiparallel beta-strands linked by three ordered loops. A single zinc ion is coordinated by four conserved cysteines from the first and third loops, which form two rubredoxin knuckles. Npl4 NZF binds specifically, but weakly, to free ubiquitin using a conserved 13TF14 dipeptide to interact with the "Ile-44" surface of ubiquitin. Our studies reveal the structure of this versatile class of protein binding domains and provide a means for identifying the subset of NZF domains likely to bind ubiquitin.

-	~~{{STRUCTURE_1nj3\| PDB=1nj3 \| SCENE= }}~~	+	Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.,Wang B, Alam SL, Meyer HH, Payne M, Stemmler TL, Davis DR, Sundquist WI J Biol Chem. 2003 May 30;278(22):20225-34. Epub 2003 Mar 18. PMID:12644454<ref>PMID:12644454</ref>

-	~~===Structure and Ubiquitin Interactions~~ of the ~~Conserved NZF Domain of Npl4===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12644454}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1nj3]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012644454<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Alam, S L.]]		[[Category: Alam, S L.]]

OCA: Protected "1nj3" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:40:59 GMT

Protected "1nj3" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:40, 5 December 2012

OCA at 19:40, 5 December 2012

OCA — Wed, 05 Dec 2012 19:40:56 GMT

←Older revision		Revision as of 19:40, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nj3.png\|left\|200px]]		[[Image:1nj3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nj3", 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_1nj3\| PDB=1nj3 \| SCENE= }}		{{STRUCTURE_1nj3\| PDB=1nj3 \| SCENE= }}

	===Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4===		===Structure and Ubiquitin Interactions of the Conserved NZF Domain of Npl4===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12644454}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12644454 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12644454}}		{{ABSTRACT_PUBMED_12644454}}

	==About this Structure==		==About this Structure==
-	~~1NJ3~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA].	+	[[1nj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12644454~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012644454</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Alam, S L.]]		[[Category: Alam, S L.]]
Line 35:		Line 23:
	[[Category: Npl4]]		[[Category: Npl4]]
	[[Category: Nzf domain]]		[[Category: Nzf domain]]
		+	[[Category: Protein binding]]
	[[Category: Rubredoxin knuckle]]		[[Category: Rubredoxin knuckle]]
	[[Category: Ubiquitin]]		[[Category: Ubiquitin]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:56:39 2009''

OCA at 01:56, 18 February 2009

OCA — Wed, 18 Feb 2009 01:56:39 GMT

←Older revision		Revision as of 01:56, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1NJ3 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA].	+	1NJ3 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJ3 OCA].

	==Reference==		==Reference==
-	Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4., Wang B, Alam SL, Meyer HH, Payne M, Stemmler TL, Davis DR, Sundquist WI, J Biol Chem. 2003 May 30;278(22):20225-34. Epub 2003 Mar 18. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12644454 12644454]~~	+	<ref group="xtra">PMID:12644454</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Single protein]]
	[[Category: Alam, S L.]]		[[Category: Alam, S L.]]
	[[Category: Davis, D R.]]		[[Category: Davis, D R.]]
Line 40:		Line 39:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 10~~:06:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:56:39 2009''