3ddk - Revision history

OCA at 12:45, 30 August 2023

OCA — Wed, 30 Aug 2023 12:45:40 GMT

←Older revision		Revision as of 12:45, 30 August 2023
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	<StructureSection load='3ddk' size='340' side='right'caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3ddk' size='340' side='right'caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Coxsackievirus_b3~~ Coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_B3 Coxsackievirus B3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.25Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~3Dpol ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=12072 Coxsackievirus B3])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [https://pdbe.org/3ddk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [https://www.ebi.ac.uk/pdbsum/3ddk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddk 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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [https://pdbe.org/3ddk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [https://www.ebi.ac.uk/pdbsum/3ddk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q66338_9ENTO Q66338_9ENTO]] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS001676_004_016611] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS001676_004_010047]	+	[https://www.uniprot.org/uniprot/Q5UEA2_9ENTO Q5UEA2_9ENTO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Coxsackievirus b3]]	+	[[Category: Coxsackievirus B3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campagnola, G]]	+	[[Category: Campagnola G]]
-	[[Category: Peersen~~, O B~~]]	+	[[Category: Peersen OB]]
-	[[Category: Scoggin~~, K E~~]]	+	[[Category: Scoggin KE]]
-	[[Category: Weygandt~~, M H]]~~	+	[[Category: Weygandt MH]]
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Rna virus]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Viral polymerase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:56, 9 February 2022

OCA — Wed, 09 Feb 2022 07:56:27 GMT

←Older revision		Revision as of 07:56, 9 February 2022
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	==Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase==		==Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase==
-	<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='3ddk' size='340' side='right'caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Coxsackievirus_b3 Coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_b3 Coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Coxsackievirus B3])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Coxsackievirus B3])</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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [~~http~~://pdbe.org/3ddk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ddk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddk 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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [https://pdbe.org/3ddk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [https://www.ebi.ac.uk/pdbsum/3ddk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q66338_9ENTO Q66338_9ENTO]] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS001676_004_016611] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS001676_004_010047]	+	[[https://www.uniprot.org/uniprot/Q66338_9ENTO Q66338_9ENTO]] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS001676_004_016611] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS001676_004_010047]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddk_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3ddk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ddk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Coxsackievirus b3]]		[[Category: Coxsackievirus b3]]
		+	[[Category: Large Structures]]
	[[Category: Campagnola, G]]		[[Category: Campagnola, G]]
	[[Category: Peersen, O B]]		[[Category: Peersen, O B]]

OCA at 08:47, 25 October 2017

OCA — Wed, 25 Oct 2017 08:47:38 GMT

←Older revision		Revision as of 08:47, 25 October 2017
Line 1:		Line 1:
		+
	==Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase==		==Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase==
	<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Coxsackievirus B3])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Coxsackievirus B3])</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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://pdbe.org/3ddk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk 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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://pdbe.org/3ddk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3ddk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ddk" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:10, 8 February 2016

OCA — Mon, 08 Feb 2016 09:10:31 GMT

←Older revision		Revision as of 09:10, 8 February 2016
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	<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_coxsackievirus_b3 Human coxsackievirus~~ b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_b3 Coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 ~~Human coxsackievirus~~ B3])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Coxsackievirus B3])</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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk 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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://pdbe.org/3ddk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3ddk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3ddk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human coxsackievirus~~ b3]]	+	[[Category: Coxsackievirus b3]]
	[[Category: Campagnola, G]]		[[Category: Campagnola, G]]
	[[Category: Peersen, O B]]		[[Category: Peersen, O B]]

OCA at 22:12, 24 December 2014

OCA — Wed, 24 Dec 2014 22:12:28 GMT

←Older revision		Revision as of 22:12, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Human coxsackievirus B3])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Human coxsackievirus B3])</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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk 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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q66338_9ENTO Q66338_9ENTO]] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS001676_004_016611] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS001676_004_010047]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human coxsackievirus b3]]		[[Category: Human coxsackievirus b3]]
-	[[Category: Campagnola, G.]]	+	[[Category: Campagnola, G]]
-	[[Category: Peersen, O B.]]	+	[[Category: Peersen, O B]]
-	[[Category: Scoggin, K E.]]	+	[[Category: Scoggin, K E]]
-	[[Category: Weygandt, M H.]]	+	[[Category: Weygandt, M H]]
	[[Category: Rna polymerase]]		[[Category: Rna polymerase]]
	[[Category: Rna virus]]		[[Category: Rna virus]]

OCA at 10:57, 29 September 2014

OCA — Mon, 29 Sep 2014 10:57:07 GMT

←Older revision		Revision as of 10:57, 29 September 2014
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-	[[~~Image:~~3ddk.~~png~~\|~~left~~\|200px]]	+	==Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase==
		+	<StructureSection load='3ddk' size='340' side='right' caption='[[3ddk]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">3Dpol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12072 Human coxsackievirus B3])</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=3ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ddk RCSB], [http://www.ebi.ac.uk/pdbsum/3ddk 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/dd/3ddk_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 crystal structure of the coxsackievirus B3 polymerase has been solved at 2.25-A resolution and is shown to be highly homologous to polymerases from poliovirus, rhinovirus, and foot-and-mouth disease viruses. Together, these structures highlight several conserved structural elements in picornaviral polymerases, including a proteolytic activation-dependent N-terminal structure that is essential for full activity. Interestingly, a comparison of all of the picornaviral polymerase structures shows an unusual conformation for residue 5, which is always located at a distortion in the beta-strand composed of residues 1 to 8. In our earlier structure of the poliovirus polymerase, we attributed this conformation to a crystal packing artifact, but the observation that this conformation is conserved among picornaviruses led us to examine the role of this residue in further detail. Here we use coxsackievirus polymerase to show that elongation activity correlates with the hydrophobicity of residue 5 and, surprisingly, more hydrophobic residues result in higher activity. Based on structural analysis, we propose that this residue becomes buried during the nucleotide repositioning step that occurs prior to phosphoryl transfer. We present a model in which the buried N terminus observed in all picornaviral polymerases is essential for stabilizing the structure during this conformational change.

-	~~{{STRUCTURE_3ddk\| PDB=3ddk \| SCENE= }}~~	+	Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases.,Campagnola G, Weygandt M, Scoggin K, Peersen O J Virol. 2008 Oct;82(19):9458-64. Epub 2008 Jul 16. PMID:18632862<ref>PMID:18632862</ref>

-	~~===Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18632862}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ddk]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018632862<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human coxsackievirus b3]]		[[Category: Human coxsackievirus b3]]
	[[Category: Campagnola, G.]]		[[Category: Campagnola, G.]]

OCA at 09:39, 20 October 2012

OCA — Sat, 20 Oct 2012 09:39:37 GMT

←Older revision		Revision as of 09:39, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3ddk]] is a 1 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Human_coxsackievirus~~ Human coxsackievirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].	+	[[3ddk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].

	==See Also==		==See Also==
Line 15:		Line 15:
	==Reference==		==Reference==
	<ref group="xtra">PMID:018632862</ref><references group="xtra"/>		<ref group="xtra">PMID:018632862</ref><references group="xtra"/>
-	[[Category: Human coxsackievirus]]	+	[[Category: Human coxsackievirus b3]]
	[[Category: Campagnola, G.]]		[[Category: Campagnola, G.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]

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

OCA — Wed, 25 Jul 2012 23:34:59 GMT

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

←Older revision

Revision as of 23:34, 25 July 2012

OCA at 23:34, 25 July 2012

OCA — Wed, 25 Jul 2012 23:34:57 GMT

←Older revision		Revision as of 23:34, 25 July 2012
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-	{{Seed}}
	[[Image:3ddk.png\|left\|200px]]		[[Image:3ddk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ddk", 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_3ddk\| PDB=3ddk \| SCENE= }}		{{STRUCTURE_3ddk\| PDB=3ddk \| SCENE= }}

	===Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase===		===Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18632862}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18632862 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18632862}}		{{ABSTRACT_PUBMED_18632862}}

	==About this Structure==		==About this Structure==
-	~~3DDK~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Human_coxsackievirus_b3~~ Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].	+	[[3ddk]] is a 1 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus Human coxsackievirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18632862~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018632862</ref><references group="xtra"/>
-	[[Category: Human coxsackievirus b3]]	+	[[Category: Human coxsackievirus]]
	[[Category: Campagnola, G.]]		[[Category: Campagnola, G.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]
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	[[Category: Viral polymerase]]		[[Category: Viral polymerase]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:52:03 2009''

OCA at 18:52, 16 February 2009

OCA — Mon, 16 Feb 2009 18:52:04 GMT

←Older revision		Revision as of 18:52, 16 February 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3ddk.~~jpg~~\|left\|200px]]	+	[[Image:3ddk.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	3DDK is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].	+	3DDK is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Human_coxsackievirus_b3 Human coxsackievirus b3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDK OCA].

	==Reference==		==Reference==
-	Crystal structure of coxsackievirus B3 3Dpol highlights the functional importance of residue 5 in picornavirus polymerases., Campagnola G, Weygandt M, Scoggin K, Peersen O, J Virol. 2008 Oct;82(19):9458-64. Epub 2008 Jul 16. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18632862 18632862]~~	+	<ref group="xtra">PMID:18632862</ref><references group="xtra"/>
	[[Category: Human coxsackievirus b3]]		[[Category: Human coxsackievirus b3]]
-	[[Category: Single protein]]
	[[Category: Campagnola, G.]]		[[Category: Campagnola, G.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]
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	[[Category: Viral protein]]		[[Category: Viral protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Sep 24 10~~:41:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:52:03 2009''