5m3j - Revision history

OCA at 18:23, 1 November 2023

OCA — Wed, 01 Nov 2023 18:23:42 GMT

←Older revision		Revision as of 18:23, 1 November 2023
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	<StructureSection load='5m3j' size='340' side='right'caption='[[5m3j]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5m3j' size='340' side='right'caption='[[5m3j]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m3j]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Influenza_b_virus_~~(b/~~memphis~~/13/03) Influenza b virus (b/~~memphis~~/13/03)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m3j]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Influenza_B_virus Influenza B virus] and [https://en.wikipedia.org/wiki/Influenza_B_virus_(B/Memphis/13/2003) Influenza B virus (B/Memphis/13/2003)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M3J FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]] 3.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PA ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&id=1601067 Influenza B virus (B/Memphis/13/03)]), PB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1601067 Influenza B virus (B/Memphis/13/03)]), PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1601067 Influenza B virus (B/Memphis/13/03)])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [https://pdbe.org/5m3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [https://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [~~http~~://pdbe.org/5m3j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5V8Z9_9INFB Q5V8Z9_9INFB]
	<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: Homo sapiens]]
		+	[[Category: Influenza B virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RNA-directed RNA polymerase]]~~	+	[[Category: Cusack S]]
-	[[Category: Cusack, S]]	+	[[Category: Lukarska M]]
-	[[Category: Lukarska, M]]	+	[[Category: Pflug A]]
-	[[Category: Pflug, A]]	+
-	~~[[Category: Influenza b virus rna-dependent rna polymerase]]~~	+
-	~~[[Category: Pol ii serine 5 phosphorylated ctd peptide]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Vrna promoter~~]]	+

OCA at 11:00, 12 August 2020

OCA — Wed, 12 Aug 2020 11:00:18 GMT

←Older revision		Revision as of 11:00, 12 August 2020
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	==Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD==		==Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD==
-	<StructureSection load='5m3j' size='340' side='right' caption='[[5m3j]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5m3j' size='340' side='right'caption='[[5m3j]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m3j]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M3J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m3j]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Influenza_b_virus_(b/memphis/13/03) Influenza b virus (b/memphis/13/03)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M3J FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1601067 Influenza B virus (B/Memphis/13/03)]), PB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1601067 Influenza B virus (B/Memphis/13/03)]), PB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1601067 Influenza B virus (B/Memphis/13/03)])</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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [http://pdbe.org/5m3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [http://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [http://pdbe.org/5m3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [http://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5m3j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5m3j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]
	[[Category: Cusack, S]]		[[Category: Cusack, S]]

OCA at 07:22, 18 January 2017

OCA — Wed, 18 Jan 2017 07:22:24 GMT

←Older revision		Revision as of 07:22, 18 January 2017
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	<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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [http://pdbe.org/5m3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [http://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j 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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [http://pdbe.org/5m3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [http://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The heterotrimeric influenza polymerase (FluPol), comprising subunits PA, PB1 and PB2, binds to the conserved 5' and 3' termini (the 'promoter') of each of the eight single-stranded viral RNA (vRNA) genome segments and performs both transcription and replication of vRNA in the infected cell nucleus. To transcribe viral mRNAs, FluPol associates with cellular RNA polymerase II (Pol II), which enables it to take 5'-capped primers from nascent Pol II transcripts. Here we present a co-crystal structure of bat influenza A polymerase bound to a Pol II C-terminal domain (CTD) peptide mimic, which shows two distinct phosphoserine-5 (SeP5)-binding sites in the polymerase PA subunit, accommodating four CTD heptad repeats overall. Mutagenesis of the SeP5-contacting basic residues (PA K289, R454, K635 and R638) weakens CTD repeat binding in vitro without affecting the intrinsic cap-primed (transcription) or unprimed (replication) RNA synthesis activity of recombinant polymerase, whereas in cell-based minigenome assays the same mutations substantially reduce overall polymerase activity. Only recombinant viruses with a single mutation in one of the SeP5-binding sites can be rescued, but these viruses are severely attenuated and genetically unstable. Several previously described mutants that modulate virulence can be rationalized by our results, including a second site mutation (PA(C453R)) that enables the highly attenuated mutant virus (PA(R638A)) to revert to near wild-type infectivity. We conclude that direct binding of FluPol to the SeP5 Pol II CTD is fine-tuned to allow efficient viral transcription and propose that the CTD-binding site on FluPol could be targeted for antiviral drug development.
		+
		+	Structural basis of an essential interaction between influenza polymerase and Pol II CTD.,Lukarska M, Fournier G, Pflug A, Resa-Infante P, Reich S, Naffakh N, Cusack S Nature. 2017 Jan 5;541(7635):117-121. doi: 10.1038/nature20594. Epub 2016 Dec 21. PMID:28002402<ref>PMID:28002402</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5m3j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:44, 22 December 2016

OCA — Thu, 22 Dec 2016 21:44:52 GMT

←Older revision		Revision as of 21:44, 22 December 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5m3j is ~~ON HOLD until Paper Publication~~	+	==Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD==
-		+	<StructureSection load='5m3j' size='340' side='right' caption='[[5m3j]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5m3j]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M3J FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5m3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m3j OCA], [http://pdbe.org/5m3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m3j RCSB], [http://www.ebi.ac.uk/pdbsum/5m3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m3j ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA-directed RNA polymerase]]
		+	[[Category: Cusack, S]]
		+	[[Category: Lukarska, M]]
		+	[[Category: Pflug, A]]
		+	[[Category: Influenza b virus rna-dependent rna polymerase]]
		+	[[Category: Pol ii serine 5 phosphorylated ctd peptide]]
		+	[[Category: Viral protein]]
		+	[[Category: Vrna promoter]]

OCA at 16:21, 9 December 2016

OCA — Fri, 09 Dec 2016 16:21:17 GMT

←Older revision		Revision as of 16:21, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5m3j is ON HOLD	+	The entry 5m3j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5m3j" [edit=sysop:move=sysop]

OCA — Wed, 26 Oct 2016 16:21:08 GMT

Protected "5m3j" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:21, 26 October 2016

OCA: New page: '''Unreleased structure''' The entry 5m3j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Oct 2016 16:21:07 GMT

New page: '''Unreleased structure''' The entry 5m3j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5m3j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]