6u1x - Revision history

OCA at 09:28, 20 March 2024

2024-03-20T09:28:23Z

←Older revision		Revision as of 09:28, 20 March 2024
Line 3:		Line 3:
	<SX load='6u1x' size='340' side='right' viewer='molstar' caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>		<SX load='6u1x' size='340' side='right' viewer='molstar' caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6U1X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vesicular_stomatitis_Indiana_virus_strain_San_Juan Vesicular stomatitis Indiana virus strain San Juan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U1X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3Å</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=6u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1x OCA], [~~http~~://pdbe.org/6u1x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u1x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u1x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1x ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1x OCA], [https://pdbe.org/6u1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u1x RCSB], [https://www.ebi.ac.uk/pdbsum/6u1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/L_VSIVA L_VSIVA]] RNA-directed RNA polymerase that catalyzes the transcription of viral mRNAs, their caping and polyadenylation (PubMed:24526687). The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at the 3' leader promoter, and transcribes subsequently all viral mRNAs with a decreasing efficiency. The first gene is the most transcribed, and the last the least transcribed. The viral phosphoprotein acts as a processivity factor (PubMed:22908284). Caping is concommitant with initiation of mRNA transcription. The polymerase mRNA guanylyl transferase displays a different biochemical reaction than the cellular enzyme (PubMed:21945214). Polyadenylation of mRNAs occur by a stuttering mechanism at a slipery stop site present at the end viral genes. After finishing transcription of a mRNA, the polymerase can resume transcription of the downstream gene.<ref>PMID:2171304</ref> <ref>PMID:21945214</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref> RNA-directed RNA polymerase that catalyzes the replication of viral genomic RNA. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing transcriptional signals, and the replicated genome is not caped or polyadenylated.<ref>PMID:2171304</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref> [[http://www.uniprot.org/uniprot/PHOSP_VSIVA PHOSP_VSIVA]] Essential component of the RNA polymerase transcription and replication complex. Binds the viral ribonucleocapsid and positions the L polymerase on the template. May act as a chaperone for newly synthesized free N protein, so-called N(0). Plays a role in virion assembly.<ref>PMID:8676480</ref> <ref>PMID:15163735</ref> <ref>PMID:15956555</ref>	+	[https://www.uniprot.org/uniprot/L_VSIVA L_VSIVA] RNA-directed RNA polymerase that catalyzes the transcription of viral mRNAs, their caping and polyadenylation (PubMed:24526687). The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at the 3' leader promoter, and transcribes subsequently all viral mRNAs with a decreasing efficiency. The first gene is the most transcribed, and the last the least transcribed. The viral phosphoprotein acts as a processivity factor (PubMed:22908284). Caping is concommitant with initiation of mRNA transcription. The polymerase mRNA guanylyl transferase displays a different biochemical reaction than the cellular enzyme (PubMed:21945214). Polyadenylation of mRNAs occur by a stuttering mechanism at a slipery stop site present at the end viral genes. After finishing transcription of a mRNA, the polymerase can resume transcription of the downstream gene.<ref>PMID:2171304</ref> <ref>PMID:21945214</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref> RNA-directed RNA polymerase that catalyzes the replication of viral genomic RNA. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing transcriptional signals, and the replicated genome is not caped or polyadenylated.<ref>PMID:2171304</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 A resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide.	+

-	Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor.,Jenni S, Bloyet LM, Diaz-Avalos R, Liang B, Whelan SPJ, Grigorieff N, Harrison SC Cell Rep. 2020 Jan 7;30(1):53-60.e5. doi: 10.1016/j.celrep.2019.12.024. PMID:31914397<ref>PMID:31914397</ref>	+	==See Also==
-		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6u1x" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
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	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bloyet~~, L M~~]]	+	[[Category: Vesicular stomatitis Indiana virus strain San Juan]]
-	[[Category: Dias-Avalos, R]]	+	[[Category: Bloyet LM]]
-	[[Category: Grigorieff, N]]	+	[[Category: Dias-Avalos R]]
-	[[Category: Harrison~~, S C~~]]	+	[[Category: Grigorieff N]]
-	[[Category: Jenni, S]]	+	[[Category: Harrison SC]]
-	[[Category: Liang, B]]	+	[[Category: Jenni S]]
-	[[Category: Wheelman~~, S P.J]]~~	+	[[Category: Liang B]]
-	~~[[Category: L protein]]~~	+	[[Category: Wheelman SPJ]]
-	~~[[Category: Nonsegmented negative-sense rna viruse]]~~	+
-	~~[[Category: P protein]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Prntase]]~~	+
-	~~[[Category: Rdrp]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Rna-dependent rna polymerase]]~~	+
-	~~[[Category: Single particle analysis]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Vesicular stomatitis virus]]~~	+
-	~~[[Category: Viral]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 06:37, 11 April 2020

2020-04-11T06:37:49Z

←Older revision		Revision as of 06:37, 11 April 2020
Line 3:		Line 3:
	<SX load='6u1x' size='340' side='right' viewer='molstar' caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>		<SX load='6u1x' size='340' side='right' viewer='molstar' caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U1X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U1X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1x OCA], [http://pdbe.org/6u1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1x RCSB], [http://www.ebi.ac.uk/pdbsum/6u1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1x 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=6u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1x OCA], [http://pdbe.org/6u1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1x RCSB], [http://www.ebi.ac.uk/pdbsum/6u1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 01:04, 7 March 2020

2020-03-07T01:04:48Z

←Older revision		Revision as of 01:04, 7 March 2020
Line 1:		Line 1:

	==Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)==		==Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)==
-	<~~StructureSection~~ load='6u1x' size='340' side='right'caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<SX load='6u1x' size='340' side='right' viewer='molstar' caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U1X FirstGlance]. <br>		<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U1X FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bloyet, L M]]		[[Category: Bloyet, L M]]

OCA at 16:21, 22 January 2020

2020-01-22T16:21:37Z

←Older revision		Revision as of 16:21, 22 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u1x is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution)==
		+	<StructureSection load='6u1x' size='340' side='right'caption='[[6u1x]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6u1x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U1X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u1x OCA], [http://pdbe.org/6u1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u1x RCSB], [http://www.ebi.ac.uk/pdbsum/6u1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u1x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/L_VSIVA L_VSIVA]] RNA-directed RNA polymerase that catalyzes the transcription of viral mRNAs, their caping and polyadenylation (PubMed:24526687). The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The viral polymerase binds to the genomic RNA at the 3' leader promoter, and transcribes subsequently all viral mRNAs with a decreasing efficiency. The first gene is the most transcribed, and the last the least transcribed. The viral phosphoprotein acts as a processivity factor (PubMed:22908284). Caping is concommitant with initiation of mRNA transcription. The polymerase mRNA guanylyl transferase displays a different biochemical reaction than the cellular enzyme (PubMed:21945214). Polyadenylation of mRNAs occur by a stuttering mechanism at a slipery stop site present at the end viral genes. After finishing transcription of a mRNA, the polymerase can resume transcription of the downstream gene.<ref>PMID:2171304</ref> <ref>PMID:21945214</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref> RNA-directed RNA polymerase that catalyzes the replication of viral genomic RNA. The template is composed of the viral RNA tightly encapsidated by the nucleoprotein (N). The replicase mode is dependent on intracellular N protein concentration. In this mode, the polymerase replicates the whole viral genome without recognizing transcriptional signals, and the replicated genome is not caped or polyadenylated.<ref>PMID:2171304</ref> <ref>PMID:22246179</ref> <ref>PMID:22908284</ref> <ref>PMID:24526687</ref> [[http://www.uniprot.org/uniprot/PHOSP_VSIVA PHOSP_VSIVA]] Essential component of the RNA polymerase transcription and replication complex. Binds the viral ribonucleocapsid and positions the L polymerase on the template. May act as a chaperone for newly synthesized free N protein, so-called N(0). Plays a role in virion assembly.<ref>PMID:8676480</ref> <ref>PMID:15163735</ref> <ref>PMID:15956555</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 A resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide.

-	~~Authors~~:	+	Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor.,Jenni S, Bloyet LM, Diaz-Avalos R, Liang B, Whelan SPJ, Grigorieff N, Harrison SC Cell Rep. 2020 Jan 7;30(1):53-60.e5. doi: 10.1016/j.celrep.2019.12.024. PMID:31914397<ref>PMID:31914397</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6u1x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bloyet, L M]]
		+	[[Category: Dias-Avalos, R]]
		+	[[Category: Grigorieff, N]]
		+	[[Category: Harrison, S C]]
		+	[[Category: Jenni, S]]
		+	[[Category: Liang, B]]
		+	[[Category: Wheelman, S P.J]]
		+	[[Category: L protein]]
		+	[[Category: Nonsegmented negative-sense rna viruse]]
		+	[[Category: P protein]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Prntase]]
		+	[[Category: Rdrp]]
		+	[[Category: Replication]]
		+	[[Category: Rna-dependent rna polymerase]]
		+	[[Category: Single particle analysis]]
		+	[[Category: Transcription]]
		+	[[Category: Vesicular stomatitis virus]]
		+	[[Category: Viral]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus]]

OCA at 08:06, 2 October 2019

2019-10-02T08:06:56Z

←Older revision		Revision as of 08:06, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u1x is ON HOLD	+	The entry 6u1x is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6u1x" [edit=sysop:move=sysop]

2019-08-28T14:02:04Z

Protected "6u1x" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:02, 28 August 2019

OCA: New page: '''Unreleased structure''' The entry 6u1x is ON HOLD Authors: Description: Category: Unreleased Structures

2019-08-28T14:02:02Z

New page: '''Unreleased structure''' The entry 6u1x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6u1x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]