6o3v - Revision history

OCA at 14:50, 13 March 2024

OCA — Wed, 13 Mar 2024 14:50:26 GMT

←Older revision		Revision as of 14:50, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o3v' size='340' side='right'caption='[[6o3v]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6o3v' size='340' side='right'caption='[[6o3v]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o3v]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Group_a_rotaviruses Group a rotaviruses~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6O3V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o3v]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rotavirus_A Rotavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O3V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">VP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28875 Group A rotaviruses])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6o3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3v OCA], [~~http~~://pdbe.org/6o3v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o3v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o3v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3v 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=6o3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3v OCA], [https://pdbe.org/6o3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o3v RCSB], [https://www.ebi.ac.uk/pdbsum/6o3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q1WK45_9REOV Q1WK45_9REOV~~]] Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated.[HAMAP-Rule:MF_04128] Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 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 capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not.[HAMAP-Rule:MF_04128]	+	[https://www.uniprot.org/uniprot/Q1WK45_9VIRU Q1WK45_9VIRU]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo-electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.	+

-	2.7 A cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity.,Kumar D, Yu X, Crawford SE, Moreno R, Jakana J, Sankaran B, Anish R, Kaundal S, Hu L, Estes MK, Wang Z, Prasad BVV Sci Adv. 2020 Apr 15;6(16):eaay6410. doi: 10.1126/sciadv.aay6410. eCollection, 2020 Apr. PMID:32494598<ref>PMID:32494598</ref>	+	==See Also==
-		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6o3v" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Group a rotaviruses]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hu, L]]	+	[[Category: Rotavirus A]]
-	[[Category: Kumar, D]]	+	[[Category: Hu L]]
-	[[Category: Prasad, V]]	+	[[Category: Kumar D]]
-	[[Category: Wang, Z]]	+	[[Category: Prasad V]]
-	[[Category: Yu, X]]	+	[[Category: Wang Z]]
-	~~[[Category: Capping enzyme]]~~	+	[[Category: Yu X]]
-	~~[[Category: Guanylyl transferase]]~~	+
-	~~[[Category: Methyl transferase]]~~	+
-	~~[[Category: Pde]]~~	+
-	~~[[Category: Rotavirus]]~~	+
-	~~[[Category: Rtpase]]~~	+
-	~~[[Category: Structural protein]]~~	+
-	~~[[Category: Vp3~~]]	+

OCA at 10:05, 16 September 2020

OCA — Wed, 16 Sep 2020 10:05:59 GMT

←Older revision		Revision as of 10:05, 16 September 2020
Line 3:		Line 3:
	<StructureSection load='6o3v' size='340' side='right'caption='[[6o3v]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6o3v' size='340' side='right'caption='[[6o3v]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o3v]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O3V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o3v]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Group_a_rotaviruses Group a rotaviruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6O3V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6o3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3v OCA], [http://pdbe.org/6o3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o3v RCSB], [http://www.ebi.ac.uk/pdbsum/6o3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3v ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28875 Group A rotaviruses])</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=6o3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3v OCA], [http://pdbe.org/6o3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o3v RCSB], [http://www.ebi.ac.uk/pdbsum/6o3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q1WK45_9REOV Q1WK45_9REOV]] Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated.[HAMAP-Rule:MF_04128] Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 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 capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not.[HAMAP-Rule:MF_04128]		[[http://www.uniprot.org/uniprot/Q1WK45_9REOV Q1WK45_9REOV]] Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated.[HAMAP-Rule:MF_04128] Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 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 capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not.[HAMAP-Rule:MF_04128]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo-electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.
		+
		+	2.7 A cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity.,Kumar D, Yu X, Crawford SE, Moreno R, Jakana J, Sankaran B, Anish R, Kaundal S, Hu L, Estes MK, Wang Z, Prasad BVV Sci Adv. 2020 Apr 15;6(16):eaay6410. doi: 10.1126/sciadv.aay6410. eCollection, 2020 Apr. PMID:32494598<ref>PMID:32494598</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6o3v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Group a rotaviruses]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hu, L]]		[[Category: Hu, L]]

OCA at 06:43, 4 March 2020

OCA — Wed, 04 Mar 2020 06:43:38 GMT

←Older revision		Revision as of 06:43, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6o3v is ~~ON HOLD until Paper Publication~~	+	==Crystal structure for RVA-VP3==
-		+	<StructureSection load='6o3v' size='340' side='right'caption='[[6o3v]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6o3v]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O3V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O3V FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6o3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o3v OCA], [http://pdbe.org/6o3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o3v RCSB], [http://www.ebi.ac.uk/pdbsum/6o3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o3v ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q1WK45_9REOV Q1WK45_9REOV]] Counteracts the host innate immune response thanks to its phosphodiesterase that degrades the 5'-triphosphorylated, 2'-5' linked adenylate oligomers produced by the host cell IFN-inducible 2',5'-oligoadenylate synthetase (OAS). The host RNaseL is therefore not activated.[HAMAP-Rule:MF_04128] Multifunctional enzyme involved in mRNA capping. Catalyzes the formation of the 5' cap structure on the viral plus-strand transcripts. Specifically binds to GTP and displays guanylyltransferase and methyltransferase activities. Has affinity for ssRNA but not for dsRNA. Capping activity is non-specific and caps RNAs that initiate with either a G or an A residue. Together with VP1 polymerase, forms a VP1-VP3 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 capped by VP3 and extruded through the DLP's channels into the cytoplasm where they function as mRNAs for translation of viral proteins. DLPs probably have an RNA triphosphatase activity as well, whereas open cores do not.[HAMAP-Rule:MF_04128]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hu, L]]
		+	[[Category: Kumar, D]]
		+	[[Category: Prasad, V]]
		+	[[Category: Wang, Z]]
		+	[[Category: Yu, X]]
		+	[[Category: Capping enzyme]]
		+	[[Category: Guanylyl transferase]]
		+	[[Category: Methyl transferase]]
		+	[[Category: Pde]]
		+	[[Category: Rotavirus]]
		+	[[Category: Rtpase]]
		+	[[Category: Structural protein]]
		+	[[Category: Vp3]]

OCA at 21:03, 5 June 2019

OCA — Wed, 05 Jun 2019 21:03:36 GMT

←Older revision		Revision as of 21:03, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o3v is ON HOLD	+	The entry 6o3v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 07:03, 1 May 2019

OCA — Wed, 01 May 2019 07:03:33 GMT

←Older revision		Revision as of 07:03, 1 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o3v is ON HOLD ~~until Paper Publication~~	+	The entry 6o3v is ON HOLD

	Authors:		Authors:

OCA at 10:10, 13 March 2019

OCA — Wed, 13 Mar 2019 10:10:57 GMT

←Older revision		Revision as of 10:10, 13 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o3v is ON HOLD	+	The entry 6o3v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6o3v" [edit=sysop:move=sysop]

OCA — Wed, 06 Mar 2019 05:45:34 GMT

Protected "6o3v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:45, 6 March 2019

OCA: New page: '''Unreleased structure''' The entry 6o3v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 Mar 2019 05:45:32 GMT

New page: '''Unreleased structure''' The entry 6o3v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6o3v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]