4k4y - Revision history

OCA at 12:08, 1 March 2024

OCA — Fri, 01 Mar 2024 12:08:46 GMT

←Older revision		Revision as of 12:08, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.72Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [https://pdbe.org/4k4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [https://www.ebi.ac.uk/pdbsum/4k4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4y 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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [https://pdbe.org/4k4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [https://www.ebi.ac.uk/pdbsum/4k4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q5UEA2_9ENTO Q5UEA2_9ENTO]		[https://www.uniprot.org/uniprot/Q5UEA2_9ENTO Q5UEA2_9ENTO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 A resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.
-
-	Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.,Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB PLoS One. 2013 May 8;8(5):e60272. doi: 10.1371/journal.pone.0060272. Print 2013. PMID:23667424<ref>PMID:23667424</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4k4y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:40, 30 November 2022

OCA — Wed, 30 Nov 2022 11:40:30 GMT

←Older revision		Revision as of 11:40, 30 November 2022
Line 3:		Line 3:
	<StructureSection load='4k4y' size='340' side='right'caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='4k4y' size='340' side='right'caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k4y]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cvb3 Cvb3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [https://pdbe.org/4k4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [https://www.ebi.ac.uk/pdbsum/4k4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4y ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[3ddk\|3ddk]], [[3ol6\|3ol6]], [[4k4s\|4k4s]], [[4k4t\|4k4t]], [[4k4u\|4k4u]], [[4k4v\|4k4v]], [[4k4w\|4k4w]], [[4k4x\|4k4x]], [[4k4z\|4k4z]], [[4k50\|4k50]]~~</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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [~~http~~://pdbe.org/4k4y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4k4y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4y 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/Q5UEA2_9ENTO Q5UEA2_9ENTO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cvb3~~]]	+	[[Category: Coxsackievirus B3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gong, P]]	+	[[Category: Gong P]]
-	[[Category: Peersen~~, O B]]~~	+	[[Category: Peersen OB]]
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Protein-rna complex]]~~	+
-	~~[[Category: Rna-dependent rna polymerase]]~~	+
-	~~[[Category: Transferase-rna complex~~]]	+

OCA at 09:24, 3 April 2019

OCA — Wed, 03 Apr 2019 09:24:12 GMT

←Older revision		Revision as of 09:24, 3 April 2019
Line 1:		Line 1:

	==Coxsackievirus B3 polymerase elongation complex (r2+1_form)==		==Coxsackievirus B3 polymerase elongation complex (r2+1_form)==
-	<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>	+	<StructureSection load='4k4y' size='340' side='right'caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k4y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvb3 Cvb3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
Line 27:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Coxsackievirus b3~~]]	+	[[Category: Cvb3]]
		+	[[Category: Large Structures]]
	[[Category: Gong, P]]		[[Category: Gong, P]]
	[[Category: Peersen, O B]]		[[Category: Peersen, O B]]

OCA at 17:25, 9 March 2017

OCA — Thu, 09 Mar 2017 17:25:46 GMT

←Older revision		Revision as of 17:25, 9 March 2017
Line 1:		Line 1:
		+
	==Coxsackievirus B3 polymerase elongation complex (r2+1_form)==		==Coxsackievirus B3 polymerase elongation complex (r2+1_form)==
	<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ddk\|3ddk]], [[3ol6\|3ol6]], [[4k4s\|4k4s]], [[4k4t\|4k4t]], [[4k4u\|4k4u]], [[4k4v\|4k4v]], [[4k4w\|4k4w]], [[4k4x\|4k4x]], [[4k4z\|4k4z]], [[4k50\|4k50]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ddk\|3ddk]], [[3ol6\|3ol6]], [[4k4s\|4k4s]], [[4k4t\|4k4t]], [[4k4u\|4k4u]], [[4k4v\|4k4v]], [[4k4w\|4k4w]], [[4k4x\|4k4x]], [[4k4z\|4k4z]], [[4k50\|4k50]]</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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [http://www.ebi.ac.uk/pdbsum/4k4y 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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [http://pdbe.org/4k4y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [http://www.ebi.ac.uk/pdbsum/4k4y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4k4y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:36, 20 May 2015

OCA — Wed, 20 May 2015 06:36:18 GMT

←Older revision		Revision as of 06:36, 20 May 2015
Line 2:		Line 2:
	<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human coxsackievirus~~ b3]]	+	[[Category: Coxsackievirus b3]]
	[[Category: Gong, P]]		[[Category: Gong, P]]
	[[Category: Peersen, O B]]		[[Category: Peersen, O B]]

OCA at 14:27, 25 December 2014

OCA — Thu, 25 Dec 2014 14:27:34 GMT

←Older revision		Revision as of 14:27, 25 December 2014
Line 8:		Line 8:
	<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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [http://www.ebi.ac.uk/pdbsum/4k4y 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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [http://www.ebi.ac.uk/pdbsum/4k4y 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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 14:53, 21 December 2014

OCA — Sun, 21 Dec 2014 14:53:26 GMT

←Older revision		Revision as of 14:53, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4k4y\| PDB=4k4y \| SCENE= }}~~	+	==Coxsackievirus B3 polymerase elongation complex (r2+1_form)==
-	===Coxsackievirus B3 polymerase elongation complex (r2+1_form)===	+	<StructureSection load='4k4y' size='340' side='right' caption='[[4k4y]], [[Resolution\|resolution]] 2.72Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23667424}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4k4y]] is a 16 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=4K4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ddk\|3ddk]], [[3ol6\|3ol6]], [[4k4s\|4k4s]], [[4k4t\|4k4t]], [[4k4u\|4k4u]], [[4k4v\|4k4v]], [[4k4w\|4k4w]], [[4k4x\|4k4x]], [[4k4z\|4k4z]], [[4k50\|4k50]]</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=4k4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k4y RCSB], [http://www.ebi.ac.uk/pdbsum/4k4y PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 A resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.

-	~~==Function==~~	+	Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.,Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB PLoS One. 2013 May 8;8(5):e60272. doi: 10.1371/journal.pone.0060272. Print 2013. PMID:23667424<ref>PMID:23667424</ref>
-	~~[[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]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4k4y]] is~~ a ~~16 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=4K4Y OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023667424</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human coxsackievirus b3]]		[[Category: Human coxsackievirus b3]]
-	[[Category: Gong, P.]]	+	[[Category: Gong, P]]
-	[[Category: Peersen, O B.]]	+	[[Category: Peersen, O B]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Protein-rna complex]]		[[Category: Protein-rna complex]]
	[[Category: Rna-dependent rna polymerase]]		[[Category: Rna-dependent rna polymerase]]
	[[Category: Transferase-rna complex]]		[[Category: Transferase-rna complex]]

OCA at 14:06, 3 July 2013

OCA — Wed, 03 Jul 2013 14:06:47 GMT

←Older revision		Revision as of 14:06, 3 July 2013
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4k4y]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4Y OCA].	+	[[4k4y]] is a 16 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=4K4Y OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023667424</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023667424</ref><references group="xtra"/><references/>
		+	[[Category: Human coxsackievirus b3]]
	[[Category: Gong, P.]]		[[Category: Gong, P.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]

OCA at 11:04, 3 July 2013

OCA — Wed, 03 Jul 2013 11:04:57 GMT

←Older revision		Revision as of 11:04, 3 July 2013
Line 1:		Line 1:
	{{STRUCTURE_4k4y\| PDB=4k4y \| SCENE= }}		{{STRUCTURE_4k4y\| PDB=4k4y \| SCENE= }}
	===Coxsackievirus B3 polymerase elongation complex (r2+1_form)===		===Coxsackievirus B3 polymerase elongation complex (r2+1_form)===
		+	{{ABSTRACT_PUBMED_23667424}}

	==Function==		==Function==
Line 6:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4k4y]] is a 16 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=4K4Y OCA].	+	[[4k4y]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4Y OCA].
-	~~[[Category~~: ~~Human coxsackievirus b3]]~~	+
		+	==Reference==
		+	<ref group="xtra">PMID:023667424</ref><references group="xtra"/><references/>
	[[Category: Gong, P.]]		[[Category: Gong, P.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]

OCA at 16:22, 19 June 2013

OCA — Wed, 19 Jun 2013 16:22:49 GMT

←Older revision		Revision as of 16:22, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4k4y\| PDB=4k4y \| SCENE= }}
		+	===Coxsackievirus B3 polymerase elongation complex (r2+1_form)===

-	~~The entry 4k4y~~ is ~~ON HOLD~~	+	==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]

-	~~Authors~~: Gong, P., Peersen, O.B.	+	==About this Structure==
-		+	[[4k4y]] is a 16 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=4K4Y OCA].
-	~~Description~~: ~~Coxsackievirus B3~~ polymerase ~~elongation~~ complex ~~(r2+1_form)~~	+	[[Category: Human coxsackievirus b3]]
		+	[[Category: Gong, P.]]
		+	[[Category: Peersen, O B.]]
		+	[[Category: Polymerase]]
		+	[[Category: Protein-rna complex]]
		+	[[Category: Rna-dependent rna polymerase]]
		+	[[Category: Transferase-rna complex]]