4cgs - Revision history

OCA at 17:45, 7 September 2022

OCA — Wed, 07 Sep 2022 17:45:36 GMT

←Older revision		Revision as of 17:45, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4cgs' size='340' side='right'caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4cgs' size='340' side='right'caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cgs]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dhori_thogotovirus Dhori thogotovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cgs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dhori_thogotovirus Dhori thogotovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CGS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</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=4cgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cgs OCA], [https://pdbe.org/4cgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cgs RCSB], [https://www.ebi.ac.uk/pdbsum/4cgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cgs ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4cgx\|4cgx]], [[4chc\|4chc]], [[4chd\|4chd]], [[4che\|4che]], [[4chf\|4chf]]~~</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=4cgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cgs OCA], [~~http~~://pdbe.org/4cgs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4cgs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4cgs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4cgs ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/D6PT85_9ORTO D6PT85_9ORTO]]
-	Orthomyxovirus Influenza A virus (IAV) heterotrimeric polymerase performs transcription of viral mRNAs by cap-snatching, which involves generation of capped primers by host pre-mRNA binding via the PB2 subunit cap-binding site and cleavage 10-13 nucleotides from the 5' cap by the PA subunit endonuclease. Thogotoviruses, tick-borne orthomyxoviruses that includes Thogoto (THOV), Dhori (DHOV) and Jos (JOSV) viruses, are thought to perform cap-snatching by cleaving directly after the cap and thus have no heterogeneous, host-derived sequences at the 5' extremity of their mRNAs. Based on recent work identifying the cap-binding and endonuclease domains in IAV polymerase, we determined the crystal structures of two THOV PB2 domains, the putative cap-binding and the so-called '627-domain', and the structures of the putative endonuclease domains (PA-Nter) of THOV and DHOV. Despite low sequence similarity, corresponding domains have the same fold confirming the overall architectural similarity of orthomyxovirus polymerases. However the putative Thogotovirus cap-snatching domains in PA and PB2 have non-conservative substitutions of key active site residues. Biochemical analysis confirms that, unlike the IAV domains, the THOV and DHOV PA-Nter domains do not bind divalent cations and have no endonuclease activity and the THOV central PB2 domain does not bind cap analogues. On the other hand, sequence analysis suggests that other, non-influenza, orthomyxoviruses, such as salmon anemia virus (isavirus) and Quaranfil virus likely conserve active cap-snatching domains correlating with the reported occurrence of heterogeneous, host-derived sequences at the 5' end of the mRNAs of these viruses. These results highlight the unusual nature of transcription initiation by Thogotoviruses.	+
-		+
-	Comparative structural and functional analysis of orthomyxovirus polymerase cap-snatching domains.,Guilligay D, Kadlec J, Crepin T, Lunardi T, Bouvier D, Kochs G, Ruigrok RW, Cusack S PLoS One. 2014 Jan 15;9(1):~~e84973. doi: 10.1371~~/~~journal.pone.0084973. eCollection, 2014 Jan 15. PMID:24454773<ref>PMID:24454773<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 4cgs" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Dhori thogotovirus]]		[[Category: Dhori thogotovirus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bouvier, D]]	+	[[Category: Bouvier D]]
-	[[Category: Crepin, T]]	+	[[Category: Crepin T]]
-	[[Category: Cusack, S]]	+	[[Category: Cusack S]]
-	[[Category: Guilligay, D]]	+	[[Category: Guilligay D]]
-	[[Category: Kadlec, J]]	+	[[Category: Kadlec J]]
-	[[Category: Kochs, G]]	+	[[Category: Kochs G]]
-	[[Category: Lunardi, T]]	+	[[Category: Lunardi T]]
-	[[Category: Ruigrok~~, R W.H]]~~	+	[[Category: Ruigrok RWH]]
-	~~[[Category: Transcription~~]]	+

OCA at 08:57, 20 March 2019

OCA — Wed, 20 Mar 2019 08:57:05 GMT

←Older revision		Revision as of 08:57, 20 March 2019
Line 1:		Line 1:

	==Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase==		==Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase==
-	<StructureSection load='4cgs' size='340' side='right' caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='4cgs' size='340' side='right'caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cgs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dhori_virus~~ Dhori ~~virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cgs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dhori_thogotovirus Dhori thogotovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dhori ~~virus~~]]	+	[[Category: Dhori thogotovirus]]
		+	[[Category: Large Structures]]
	[[Category: Bouvier, D]]		[[Category: Bouvier, D]]
	[[Category: Crepin, T]]		[[Category: Crepin, T]]

OCA at 22:28, 5 August 2016

OCA — Fri, 05 Aug 2016 22:28:12 GMT

←Older revision		Revision as of 22:28, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase==		==Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase==
	<StructureSection load='4cgs' size='340' side='right' caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='4cgs' size='340' side='right' caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' 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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cgx\|4cgx]], [[4chc\|4chc]], [[4chd\|4chd]], [[4che\|4che]], [[4chf\|4chf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cgx\|4cgx]], [[4chc\|4chc]], [[4chd\|4chd]], [[4che\|4che]], [[4chf\|4chf]]</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=4cgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cgs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cgs RCSB], [http://www.ebi.ac.uk/pdbsum/4cgs 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=4cgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cgs OCA], [http://pdbe.org/4cgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cgs RCSB], [http://www.ebi.ac.uk/pdbsum/4cgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cgs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4cgs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:56, 21 December 2014

OCA — Sun, 21 Dec 2014 17:56:21 GMT

←Older revision		Revision as of 17:56, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4cgs\| PDB=4cgs \| SCENE= }}~~	+	==Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase==
-	===Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase===	+	<StructureSection load='4cgs' size='340' side='right' caption='[[4cgs]], [[Resolution\|resolution]] 1.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24454773}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4cgs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dhori_virus Dhori virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CGS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cgx\|4cgx]], [[4chc\|4chc]], [[4chd\|4chd]], [[4che\|4che]], [[4chf\|4chf]]</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=4cgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cgs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cgs RCSB], [http://www.ebi.ac.uk/pdbsum/4cgs PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orthomyxovirus Influenza A virus (IAV) heterotrimeric polymerase performs transcription of viral mRNAs by cap-snatching, which involves generation of capped primers by host pre-mRNA binding via the PB2 subunit cap-binding site and cleavage 10-13 nucleotides from the 5' cap by the PA subunit endonuclease. Thogotoviruses, tick-borne orthomyxoviruses that includes Thogoto (THOV), Dhori (DHOV) and Jos (JOSV) viruses, are thought to perform cap-snatching by cleaving directly after the cap and thus have no heterogeneous, host-derived sequences at the 5' extremity of their mRNAs. Based on recent work identifying the cap-binding and endonuclease domains in IAV polymerase, we determined the crystal structures of two THOV PB2 domains, the putative cap-binding and the so-called '627-domain', and the structures of the putative endonuclease domains (PA-Nter) of THOV and DHOV. Despite low sequence similarity, corresponding domains have the same fold confirming the overall architectural similarity of orthomyxovirus polymerases. However the putative Thogotovirus cap-snatching domains in PA and PB2 have non-conservative substitutions of key active site residues. Biochemical analysis confirms that, unlike the IAV domains, the THOV and DHOV PA-Nter domains do not bind divalent cations and have no endonuclease activity and the THOV central PB2 domain does not bind cap analogues. On the other hand, sequence analysis suggests that other, non-influenza, orthomyxoviruses, such as salmon anemia virus (isavirus) and Quaranfil virus likely conserve active cap-snatching domains correlating with the reported occurrence of heterogeneous, host-derived sequences at the 5' end of the mRNAs of these viruses. These results highlight the unusual nature of transcription initiation by Thogotoviruses.

-	~~==About this Structure==~~	+	Comparative structural and functional analysis of orthomyxovirus polymerase cap-snatching domains.,Guilligay D, Kadlec J, Crepin T, Lunardi T, Bouvier D, Kochs G, Ruigrok RW, Cusack S PLoS One. 2014 Jan 15;9(1):e84973. doi: 10.1371/journal.pone.0084973. eCollection, 2014 Jan 15. PMID:24454773<ref>PMID:24454773</ref>
-	~~[[4cgs]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4CGS OCA]~~.	+

-	~~==Reference==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra"~~>~~PMID:024454773~~</~~ref~~><references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Bouvier, D.]]	+	== References ==
-	[[Category: Crepin, T.]]	+	<references/>
-	[[Category: Cusack, S.]]	+	__TOC__
-	[[Category: Guilligay, D.]]	+	</StructureSection>
-	[[Category: Kadlec, J.]]	+	[[Category: Dhori virus]]
-	[[Category: Kochs, G.]]	+	[[Category: Bouvier, D]]
-	[[Category: Lunardi, T.]]	+	[[Category: Crepin, T]]
-	[[Category: Ruigrok, R W.H.]]	+	[[Category: Cusack, S]]
		+	[[Category: Guilligay, D]]
		+	[[Category: Kadlec, J]]
		+	[[Category: Kochs, G]]
		+	[[Category: Lunardi, T]]
		+	[[Category: Ruigrok, R W.H]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 11:11, 5 February 2014

OCA — Wed, 05 Feb 2014 11:11:39 GMT

←Older revision		Revision as of 11:11, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4cgs\| PDB=4cgs \| SCENE= }}
		+	===Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase===
		+	{{ABSTRACT_PUBMED_24454773}}

-	~~The entry~~ 4cgs is ~~ON HOLD~~	+	==About this Structure==
		+	[[4cgs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CGS OCA].

-	~~Authors~~: ~~Guilligay~~, D.~~, Kadlec, J.,~~ Crepin, T., ~~Lunardi, T~~.~~, Bouvier~~, D., Kochs, G., Ruigrok, R.W.H.~~, Cusack, S.~~	+	==Reference==
-		+	<ref group="xtra">PMID:024454773</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase~~	+	[[Category: Bouvier, D.]]
		+	[[Category: Crepin, T.]]
		+	[[Category: Cusack, S.]]
		+	[[Category: Guilligay, D.]]
		+	[[Category: Kadlec, J.]]
		+	[[Category: Kochs, G.]]
		+	[[Category: Lunardi, T.]]
		+	[[Category: Ruigrok, R W.H.]]
		+	[[Category: Transcription]]

OCA: Protected "4cgs" [edit=sysop:move=sysop]

OCA — Wed, 04 Dec 2013 06:31:56 GMT

Protected "4cgs" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:31, 4 December 2013

OCA: New page: '''Unreleased structure''' The entry 4cgs is ON HOLD Authors: Guilligay, D., Kadlec, J., Crepin, T., Lunardi, T., Bouvier, D., Kochs, G., Ruigrok, R.W.H., Cusack, S. Description: Cryst...

OCA — Wed, 04 Dec 2013 06:31:55 GMT

New page: '''Unreleased structure''' The entry 4cgs is ON HOLD Authors: Guilligay, D., Kadlec, J., Crepin, T., Lunardi, T., Bouvier, D., Kochs, G., Ruigrok, R.W.H., Cusack, S. Description: Cryst...

New page

'''Unreleased structure'''

The entry 4cgs is ON HOLD

Authors: Guilligay, D., Kadlec, J., Crepin, T., Lunardi, T., Bouvier, D., Kochs, G., Ruigrok, R.W.H., Cusack, S.

Description: Crystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase