7jju - Revision history

OCA at 14:52, 6 March 2024

OCA — Wed, 06 Mar 2024 14:52:30 GMT

←Older revision		Revision as of 14:52, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='7jju' size='340' side='right'caption='[[7jju]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='7jju' size='340' side='right'caption='[[7jju]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jju]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jju]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Potato_leafroll_virus Potato leafroll virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JJU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>~~, ~~<scene name='pdbligand=GZ6:Guanidinium'>GZ6</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</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]] 2.604Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=U23:'>U23</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=GZ6:Guanidinium'>GZ6</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=U23:URIDINE-5-MONOPHOSPHATE-2,3-CYCLIC+PHOSPHATE'>U23</scene></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=7jju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jju OCA], [~~http~~://pdbe.org/7jju PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jju RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jju PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jju 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=7jju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jju OCA], [https://pdbe.org/7jju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jju RCSB], [https://www.ebi.ac.uk/pdbsum/7jju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jju ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
-
-	The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold.,Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS RNA. 2020 Aug 26. pii: rna.076224.120. doi: 10.1261/rna.076224.120. PMID:32848042<ref>PMID:32848042</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7jju" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Auffinger, P]]	+	[[Category: Potato leafroll virus]]
-	[[Category: Costantino~~, D C~~]]	+	[[Category: Auffinger P]]
-	[[Category: Kieft~~, J S~~]]	+	[[Category: Costantino DC]]
-	[[Category: Nix~~, J C~~]]	+	[[Category: Kieft JS]]
-	[[Category: Steckelberg, A L]]	+	[[Category: Nix JC]]
-	[[Category: Vicens, Q]]	+	[[Category: Steckelberg A-L]]
-	~~[[Category: Rna]]~~	+	[[Category: Vicens Q]]
-	~~[[Category: Rna structure viral rna exonuclease resistance rna pseudoknot polerovirus plant virus~~]]	+

OCA at 07:17, 25 November 2020

OCA — Wed, 25 Nov 2020 07:17:23 GMT

←Older revision		Revision as of 07:17, 25 November 2020
Line 1:		Line 1:

	==Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)==		==Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)==
-	<StructureSection load='7jju' size='340' side='right'caption='[[7jju]]' scene=''>	+	<StructureSection load='7jju' size='340' side='right'caption='[[7jju]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jju]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JJU FirstGlance]. <br>
-	</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=7jju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jju OCA], [http://pdbe.org/7jju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jju RCSB], [http://www.ebi.ac.uk/pdbsum/7jju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jju ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GZ6:Guanidinium'>GZ6</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=U23:'>U23</scene></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=7jju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jju OCA], [http://pdbe.org/7jju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jju RCSB], [http://www.ebi.ac.uk/pdbsum/7jju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jju ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
		+
		+	The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold.,Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS RNA. 2020 Aug 26. pii: rna.076224.120. doi: 10.1261/rna.076224.120. PMID:32848042<ref>PMID:32848042</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jju" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Auffinger P]]	+	[[Category: Auffinger, P]]
-	[[Category: Costantino DC]]	+	[[Category: Costantino, D C]]
-	[[Category: Kieft JS]]	+	[[Category: Kieft, J S]]
-	[[Category: Nix JC]]	+	[[Category: Nix, J C]]
-	[[Category: Steckelberg A-L]]	+	[[Category: Steckelberg, A L]]
-	[[Category: Vicens Q]]	+	[[Category: Vicens, Q]]
		+	[[Category: Rna]]
		+	[[Category: Rna structure viral rna exonuclease resistance rna pseudoknot polerovirus plant virus]]

OCA at 09:37, 9 September 2020

OCA — Wed, 09 Sep 2020 09:37:53 GMT

←Older revision		Revision as of 09:37, 9 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7jju is ON HOLD until Paper Publication~~	+	==Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)==
-		+	<StructureSection load='7jju' size='340' side='right'caption='[[7jju]]' scene=''>
-	~~Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JJU FirstGlance]. <br>
-	~~Description:~~ Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)	+	</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=7jju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jju OCA], [http://pdbe.org/7jju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jju RCSB], [http://www.ebi.ac.uk/pdbsum/7jju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jju ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Costantino~~, D.C]]	+	__TOC__
-	[[Category: Auffinger, P]]	+	</StructureSection>
-	[[Category: ~~Vicens, Q~~]]	+	[[Category: Large Structures]]
-	[[Category: Kieft~~, J.S~~]]	+	[[Category: Auffinger P]]
-	[[Category: Nix~~, J.C~~]]	+	[[Category: Costantino DC]]
-	[[Category: Steckelberg, A.-L]]	+	[[Category: Kieft JS]]
		+	[[Category: Nix JC]]
		+	[[Category: Steckelberg A-L]]
		+	[[Category: Vicens Q]]

OCA at 08:27, 12 August 2020

OCA — Wed, 12 Aug 2020 08:27:36 GMT

←Older revision		Revision as of 08:27, 12 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jju is ON HOLD	+	The entry 7jju is ON HOLD until Paper Publication

	Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S.		Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S.

OCA: Protected "7jju" [edit=sysop:move=sysop]

OCA — Wed, 05 Aug 2020 04:15:54 GMT

Protected "7jju" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:15, 5 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jju is ON HOLD Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S. Description: Crystal structure of ...

OCA — Wed, 05 Aug 2020 04:15:52 GMT

New page: '''Unreleased structure''' The entry 7jju is ON HOLD Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S. Description: Crystal structure of ...

New page

'''Unreleased structure'''

The entry 7jju is ON HOLD

Authors: Steckelberg, A.-L., Vicens, Q., Auffinger, P., Costantino, D.C., Nix, J.C., Kieft, J.S.

Description: Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)
[[Category: Unreleased Structures]]
[[Category: Costantino, D.C]]
[[Category: Auffinger, P]]
[[Category: Vicens, Q]]
[[Category: Kieft, J.S]]
[[Category: Nix, J.C]]
[[Category: Steckelberg, A.-L]]