6oj4 - Revision history

OCA at 09:24, 20 March 2024

OCA — Wed, 20 Mar 2024 09:24:25 GMT

←Older revision		Revision as of 09:24, 20 March 2024
Line 3:		Line 3:
	<SX load='6oj4' size='340' side='right' viewer='molstar' caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6oj4' size='340' side='right' viewer='molstar' caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rotrh Rotrh~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_rotavirus_A_strain_RRV Simian rotavirus A strain RRV]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.3Å</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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [~~http~~://pdbe.org/6oj4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [https://pdbe.org/6oj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [https://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/B3F2X3_ROTRH B3F2X3_ROTRH]] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125] [[http://www.uniprot.org/uniprot/B3F2X2_ROTRH B3F2X2_ROTRH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[RuleBase:RU363117]	+	[https://www.uniprot.org/uniprot/B3F2X2_ROTRH B3F2X2_ROTRH] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[RuleBase:RU363117]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg(2+), and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.	+
-		+
-	In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase.,Jenni S, Salgado EN, Herrmann T, Li Z, Grant T, Grigorieff N, Trapani S, Estrozi LF, Harrison SC J Mol Biol. 2019 Jun 21. pii: S0022-2836(19)30401-2. doi:, 10.1016/j.jmb.2019.06.016. PMID:31233764<ref>PMID:31233764</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6oj4" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RNA-directed RNA polymerase]]~~	+	[[Category: Simian rotavirus A strain RRV]]
-	~~[[Category: Rotrh~~]]	+	[[Category: Estrozi LF]]
-	[[Category: Estrozi~~, L F~~]]	+	[[Category: Grant T]]
-	[[Category: Grant, T]]	+	[[Category: Grigorieff N]]
-	[[Category: Grigorieff, N]]	+	[[Category: Harrison SC]]
-	[[Category: Harrison~~, S C~~]]	+	[[Category: Herrmann T]]
-	[[Category: Herrmann, T]]	+	[[Category: Jenni S]]
-	[[Category: Jenni, S]]	+	[[Category: Li Z]]
-	[[Category: Li, Z]]	+	[[Category: Salgado EN]]
-	[[Category: Salgado~~, E N~~]]	+	[[Category: Trapani S]]
-	[[Category: Trapani, S]]	+
-	~~[[Category: Rna-dependent rna polymerase]]~~	+
-	~~[[Category: Rotavirus]]~~	+
-	~~[[Category: Viral protein-transferase complex]]~~	+
-	~~[[Category: Vp1]]~~	+
-	~~[[Category: Vp2~~]]	+

OCA at 04:01, 11 April 2020

OCA — Sat, 11 Apr 2020 04:01:26 GMT

←Older revision		Revision as of 04:01, 11 April 2020
Line 3:		Line 3:
	<SX load='6oj4' size='340' side='right' viewer='molstar' caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6oj4' size='340' side='right' viewer='molstar' caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>
	</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>		</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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [http://pdbe.org/6oj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [http://pdbe.org/6oj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:13, 6 March 2020

OCA — Fri, 06 Mar 2020 23:13:08 GMT

←Older revision		Revision as of 23:13, 6 March 2020
Line 1:		Line 1:

	==In situ structure of rotavirus VP1 RNA-dependent RNA polymerase (DLP)==		==In situ structure of rotavirus VP1 RNA-dependent RNA polymerase (DLP)==
-	<~~StructureSection~~ load='6oj4' size='340' side='right'caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<SX load='6oj4' size='340' side='right' viewer='molstar' caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]

OCA at 06:33, 10 July 2019

OCA — Wed, 10 Jul 2019 06:33:46 GMT

←Older revision		Revision as of 06:33, 10 July 2019
Line 3:		Line 3:
	<StructureSection load='6oj4' size='340' side='right'caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6oj4' size='340' side='right'caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rotavirus_a_(strain_rva/monkey/united_states/rrv/1975/g3p5b[3]) Rotavirus a (strain rva/monkey/united states/rrv/1975/g3p5b[3])~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotrh Rotrh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>
	</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>		</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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [http://pdbe.org/6oj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [http://pdbe.org/6oj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 ProSAT]</span></td></tr>
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/B3F2X3_ROTRH B3F2X3_ROTRH]] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125] [[http://www.uniprot.org/uniprot/B3F2X2_ROTRH B3F2X2_ROTRH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[RuleBase:RU363117]		[[http://www.uniprot.org/uniprot/B3F2X3_ROTRH B3F2X3_ROTRH]] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125] [[http://www.uniprot.org/uniprot/B3F2X2_ROTRH B3F2X2_ROTRH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[RuleBase:RU363117]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg(2+), and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.
		+
		+	In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase.,Jenni S, Salgado EN, Herrmann T, Li Z, Grant T, Grigorieff N, Trapani S, Estrozi LF, Harrison SC J Mol Biol. 2019 Jun 21. pii: S0022-2836(19)30401-2. doi:, 10.1016/j.jmb.2019.06.016. PMID:31233764<ref>PMID:31233764</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6oj4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]
		+	[[Category: Rotrh]]
	[[Category: Estrozi, L F]]		[[Category: Estrozi, L F]]
	[[Category: Grant, T]]		[[Category: Grant, T]]

OCA at 07:08, 24 April 2019

OCA — Wed, 24 Apr 2019 07:08:02 GMT

←Older revision		Revision as of 07:08, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6oj4 is ~~ON HOLD~~	+	==In situ structure of rotavirus VP1 RNA-dependent RNA polymerase (DLP)==
-		+	<StructureSection load='6oj4' size='340' side='right'caption='[[6oj4]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~: ~~Jenni~~, S., ~~Salgado~~, E.N., ~~Herrmann, T~~., ~~Li, Z~~., ~~Grant~~, T., ~~Grigorieff~~, N., ~~Trapani~~, S., ~~Estrozi~~, L.F., ~~Harrison, S~~.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6oj4]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotavirus_a_(strain_rva/monkey/united_states/rrv/1975/g3p5b[3]) Rotavirus a (strain rva/monkey/united states/rrv/1975/g3p5b[3])]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ4 FirstGlance]. <br>
-	~~Description: In situ structure~~ of ~~rotavirus VP1~~ RNA-~~dependent~~ RNA polymerase ~~(DLP)~~	+	</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>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj4 OCA], [http://pdbe.org/6oj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj4 ProSAT]</span></td></tr>
-	[[Category: ~~Harrison~~, ~~S.C~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B3F2X3_ROTRH B3F2X3_ROTRH]] Inner capsid protein that self-assembles to form an icosahedral capsid with a T=2 symmetry, which consists of 120 copies of VP2, with channels at each of its five-fold vertices. This capsid constitutes the innermost concentric layer of the viral mature particle. It encapsidates the polymerase VP1, the capping enzyme VP3 and the genomic dsRNA, thereby defining the core. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels formed by VP2 N-termini. VP2 is required for the replicase activity of VP1 polymerase. Probably recruits a copy of a VP1-VP3 complex, potentially along with a segment of plus-strand RNA, as a decamer of VP2 assembles. May activate the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.[RuleBase:RU363125] [[http://www.uniprot.org/uniprot/B3F2X2_ROTRH B3F2X2_ROTRH]] RNA-directed RNA polymerase that is involved in both transcription and genome replication. Together with VP3 capping enzyme, forms an enzyme complex positioned near the channels situated at each of the five-fold vertices of the core. Following infection, the outermost layer of the virus is lost, leaving a double-layered particle (DLP) made up of the core and VP6 shell. VP1 then catalyzes the transcription of fully conservative plus-strand genomic RNAs that are extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. One copy of each of the viral (+)RNAs is also recruited during core assembly, together with newly synthesized polymerase complexes and VP2. The polymerase of these novo-formed particles catalyzes the synthesis of complementary minus-strands leading to dsRNA formation. To do so, the polymerase specifically recognizes and binds 4 bases 5'-UGUG-3' in the conserved 3'-sequence of plus-strand RNA templates. VP2 presumably activates the autoinhibited VP1-RNA complex to coordinate packaging and genome replication. Once dsRNA synthesis is complete, the polymerase switches to the transcriptional mode, thus providing secondary transcription.[RuleBase:RU363117]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: RNA-directed RNA polymerase]]
		+	[[Category: Estrozi, L F]]
	[[Category: Grant, T]]		[[Category: Grant, T]]
		+	[[Category: Grigorieff, N]]
		+	[[Category: Harrison, S C]]
	[[Category: Herrmann, T]]		[[Category: Herrmann, T]]
-	[[Category: ~~Salgado~~, ~~E.N~~]]	+	[[Category: Jenni, S]]
	[[Category: Li, Z]]		[[Category: Li, Z]]
-	[[Category: ~~Jenni, S]]~~	+	[[Category: Salgado, E N]]
-	~~[[Category: Grigorieff~~, N]]	+
-	~~[[Category: Estrozi, L.F~~]]	+
	[[Category: Trapani, S]]		[[Category: Trapani, S]]
		+	[[Category: Rna-dependent rna polymerase]]
		+	[[Category: Rotavirus]]
		+	[[Category: Viral protein-transferase complex]]
		+	[[Category: Vp1]]
		+	[[Category: Vp2]]

OCA: Protected "6oj4" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2019 04:16:46 GMT

Protected "6oj4" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:16, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6oj4 is ON HOLD Authors: Jenni, S., Salgado, E.N., Herrmann, T., Li, Z., Grant, T., Grigorieff, N., Trapani, S., Estrozi, L.F., Harrison, S.C. Desc...

OCA — Wed, 17 Apr 2019 04:16:45 GMT

New page: '''Unreleased structure''' The entry 6oj4 is ON HOLD Authors: Jenni, S., Salgado, E.N., Herrmann, T., Li, Z., Grant, T., Grigorieff, N., Trapani, S., Estrozi, L.F., Harrison, S.C. Desc...

New page

'''Unreleased structure'''

The entry 6oj4 is ON HOLD

Authors: Jenni, S., Salgado, E.N., Herrmann, T., Li, Z., Grant, T., Grigorieff, N., Trapani, S., Estrozi, L.F., Harrison, S.C.

Description: In situ structure of rotavirus VP1 RNA-dependent RNA polymerase (DLP)
[[Category: Unreleased Structures]]
[[Category: Harrison, S.C]]
[[Category: Grant, T]]
[[Category: Herrmann, T]]
[[Category: Salgado, E.N]]
[[Category: Li, Z]]
[[Category: Jenni, S]]
[[Category: Grigorieff, N]]
[[Category: Estrozi, L.F]]
[[Category: Trapani, S]]