5i61 - Revision history

OCA at 08:24, 23 August 2023

2023-08-23T08:24:19Z

←Older revision		Revision as of 08:24, 23 August 2023
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	<StructureSection load='5i61' size='340' side='right'caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5i61' size='340' side='right'caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hpbvh Hpbvh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_picobirnavirus_strain_Hy005102 Human picobirnavirus strain Hy005102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I61 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5i62\|5i62]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48]~~ </~~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=5i61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i61 OCA], [https://pdbe.org/5i61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i61 RCSB], [https://www.ebi.ac.uk/pdbsum/5i61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i61 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=5i61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i61 OCA], [~~http~~://pdbe.org/5i61 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i61 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i61 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i61 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RDRP_HPBVH RDRP_HPBVH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication.	+	[https://www.uniprot.org/uniprot/RDRP_HPBVH RDRP_HPBVH] RNA-directed RNA polymerase that is involved in both transcription and genome replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hpbvh~~]]	+	[[Category: Human picobirnavirus strain Hy005102]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RNA-directed RNA polymerase]]~~	+	[[Category: Collier AM]]
-	[[Category: Collier~~, A M~~]]	+	[[Category: Guo YR]]
-	[[Category: Guo~~, Y R~~]]	+	[[Category: Tao YJ]]
-	[[Category: Tao~~, Y J]]~~	+
-	~~[[Category: Dsrna]]~~	+
-	~~[[Category: Insertion loop]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 16:15, 11 December 2019

2019-12-11T16:15:57Z

←Older revision		Revision as of 16:15, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus==		==Crystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus==
-	<StructureSection load='5i61' size='340' side='right' caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5i61' size='340' side='right'caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hpbvh Hpbvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hpbvh Hpbvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I61 FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Hpbvh]]		[[Category: Hpbvh]]
		+	[[Category: Large Structures]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]
	[[Category: Collier, A M]]		[[Category: Collier, A M]]

OCA at 17:33, 15 November 2017

2017-11-15T17:33:56Z

←Older revision		Revision as of 17:33, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5i61' size='340' side='right' caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5i61' size='340' side='right' caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hpbvh Hpbvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I61 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i62\|5i62]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i62\|5i62]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=5i61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i61 OCA], [http://pdbe.org/5i61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i61 RCSB], [http://www.ebi.ac.uk/pdbsum/5i61 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=5i61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i61 OCA], [http://pdbe.org/5i61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i61 RCSB], [http://www.ebi.ac.uk/pdbsum/5i61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i61 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hpbvh]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]
	[[Category: Collier, A M]]		[[Category: Collier, A M]]

OCA at 16:31, 10 May 2016

2016-05-10T16:31:47Z

←Older revision		Revision as of 16:31, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i61 is ~~ON HOLD~~	+	==Crystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus==
		+	<StructureSection load='5i61' size='340' side='right' caption='[[5i61]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i61]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I61 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i62\|5i62]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=5i61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i61 OCA], [http://pdbe.org/5i61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i61 RCSB], [http://www.ebi.ac.uk/pdbsum/5i61 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RDRP_HPBVH RDRP_HPBVH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 A resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.

-	~~Authors:~~ Collier, ~~A.M.~~, Guo, Y~~.R.~~, ~~Tao~~, Y.J.	+	Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus.,Collier AM, Lyytinen OL, Guo YR, Toh Y, Poranen MM, Tao YJ PLoS Pathog. 2016 Apr 14;12(4):e1005523. doi: 10.1371/journal.ppat.1005523., eCollection 2016 Apr. PMID:27078841<ref>PMID:27078841</ref>

-	~~Description: Crystal structure~~ of the RNA-~~dependent~~ RNA polymerase ~~of a human picorbirnavirus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Guo, Y.R]]	+	<div class="pdbe-citations 5i61" style="background-color:#fffaf0;"></div>
-	[[Category: Tao, Y.J]]	+	== References ==
-	[[Category: ~~Collier, A.M~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA-directed RNA polymerase]]
		+	[[Category: Collier, A M]]
		+	[[Category: Guo, Y R]]
		+	[[Category: Tao, Y J]]
		+	[[Category: Dsrna]]
		+	[[Category: Insertion loop]]
		+	[[Category: Replication]]
		+	[[Category: Transcription]]
		+	[[Category: Viral protein]]

OCA: Protected "5i61" [edit=sysop:move=sysop]

2016-02-26T16:50:05Z

Protected "5i61" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:50, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i61 is ON HOLD Authors: Collier, A.M., Guo, Y.R., Tao, Y.J. Description: Crystal structure of the RNA-dependent RNA polymerase of a human picorbir...

2016-02-26T16:50:03Z

New page: '''Unreleased structure''' The entry 5i61 is ON HOLD Authors: Collier, A.M., Guo, Y.R., Tao, Y.J. Description: Crystal structure of the RNA-dependent RNA polymerase of a human picorbir...

New page

'''Unreleased structure'''

The entry 5i61 is ON HOLD

Authors: Collier, A.M., Guo, Y.R., Tao, Y.J.

Description: Crystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus
[[Category: Unreleased Structures]]
[[Category: Guo, Y.R]]
[[Category: Tao, Y.J]]
[[Category: Collier, A.M]]