5tsk - Revision history

OCA at 15:43, 6 March 2024

OCA — Wed, 06 Mar 2024 15:43:05 GMT

←Older revision		Revision as of 15:43, 6 March 2024
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	<SX load='5tsk' size='340' side='right' viewer='molstar' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>		<SX load='5tsk' size='340' side='right' viewer='molstar' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Coxsackievirus_a16~~ Coxsackievirus ~~a16~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TSK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_A16 Coxsackievirus A16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TSK FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~5tsl~~\|~~5tsl~~]]</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]] 6.5Å</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=5tsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tsk OCA], [~~http~~://pdbe.org/5tsk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tsk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tsk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tsk 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=5tsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tsk OCA], [https://pdbe.org/5tsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tsk RCSB], [https://www.ebi.ac.uk/pdbsum/5tsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tsk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A9LXZ4_9ENTO A9LXZ4_9ENTO] Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU (By similarity). The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome (By similarity). Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2 (By similarity). During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions.[ARBA:ARBA00024846] Capsid protein VP0: Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation. Allows the capsid to remain inactive before the maturation step.[RuleBase:RU364118] Capsid protein VP1: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome. Capsid protein VP1 mainly forms the vertices of the capsid. Capsid protein VP1 interacts with host cell receptor to provide virion attachment to target host cells. This attachment induces virion internalization. Tyrosine kinases are probably involved in the entry process. After binding to its receptor, the capsid undergoes conformational changes. Capsid protein VP1 N-terminus (that contains an amphipathic alpha-helix) and capsid protein VP4 are externalized. Together, they shape a pore in the host membrane through which viral genome is translocated to host cell cytoplasm. After genome has been released, the channel shrinks.[RuleBase:RU364118] Capsid protein VP2: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome.[RuleBase:RU364118] Capsid protein VP3: Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3. The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome.[RuleBase:RU364118] Capsid protein VP4: Lies on the inner surface of the capsid shell. After binding to the host receptor, the capsid undergoes conformational changes. Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm.[RuleBase:RU364118] Component of immature procapsids, which is cleaved into capsid proteins VP4 and VP2 after maturation (By similarity). Allows the capsid to remain inactive before the maturation step.[ARBA:ARBA00025202] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (By similarity). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome.[ARBA:ARBA00025306] Lies on the inner surface of the capsid shell (By similarity). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, Capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm.[ARBA:ARBA00024643] Protease 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins.[RuleBase:RU364118] Protease 3C: Major viral protease that mediates proteolytic processing of the polyprotein. Cleaves host EIF5B, contributing to host translation shutoff. Cleaves also host PABPC1, contributing to host translation shutoff.[RuleBase:RU364118] Protein 2B: Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication.[RuleBase:RU364118] Protein 2C: Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[RuleBase:RU364118] Protein 3A: Localizes the viral replication complex to the surface of membranous vesicles. It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction. This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface.[RuleBase:RU364118] Protein 3AB: Localizes the viral replication complex to the surface of membranous vesicles. Together with protein 3CD binds the Cis-Active RNA Element (CRE) which is involved in RNA synthesis initiation. Acts as a cofactor to stimulate the activity of 3D polymerase, maybe through a nucleid acid chaperone activity.[RuleBase:RU364118] Protein 3CD: Involved in the viral replication complex and viral polypeptide maturation. It exhibits protease activity with a specificity and catalytic efficiency that is different from protease 3C. Protein 3CD lacks polymerase activity. Protein 3CD binds to the 5'UTR of the viral genome.[RuleBase:RU364118] RNA-directed RNA polymerase: Replicates the viral genomic RNA on the surface of intracellular membranes. May form linear arrays of subunits that propagate along a strong head-to-tail interaction called interface-I. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated.[RuleBase:RU364118] Viral protein genome-linked: acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU. The oriI viral genomic sequence may act as a template for this. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome.[RuleBase:RU364118]
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Coxsackievirus ~~a16~~]]	+	[[Category: Coxsackievirus A16]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cong, Y]]	+	[[Category: Cong Y]]
-	[[Category: Fan, C]]	+	[[Category: Fan C]]
-	[[Category: Huang, Z]]	+	[[Category: Huang Z]]
-	[[Category: Ye, X]]	+	[[Category: Ye X]]
-	~~[[Category: Coxsackievirus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 21:47, 10 April 2020

OCA — Fri, 10 Apr 2020 21:47:15 GMT

←Older revision		Revision as of 21:47, 10 April 2020
Line 3:		Line 3:
	<SX load='5tsk' size='340' side='right' viewer='molstar' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>		<SX load='5tsk' size='340' side='right' viewer='molstar' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TSK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TSK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tsl\|5tsl]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tsl\|5tsl]]</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=5tsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tsk OCA], [http://pdbe.org/5tsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tsk RCSB], [http://www.ebi.ac.uk/pdbsum/5tsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tsk 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=5tsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tsk OCA], [http://pdbe.org/5tsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tsk RCSB], [http://www.ebi.ac.uk/pdbsum/5tsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tsk ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 19:39, 6 March 2020

OCA — Fri, 06 Mar 2020 19:39:39 GMT

←Older revision		Revision as of 19:39, 6 March 2020
Line 1:		Line 1:

	==Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit==		==Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit==
-	<~~StructureSection~~ load='5tsk' size='340' side='right'caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>	+	<SX load='5tsk' size='340' side='right' viewer='molstar' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TSK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TSK FirstGlance]. <br>
Line 8:		Line 8:
	</table>		</table>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Coxsackievirus a16]]		[[Category: Coxsackievirus a16]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:45, 23 October 2019

OCA — Wed, 23 Oct 2019 07:45:45 GMT

←Older revision		Revision as of 07:45, 23 October 2019
Line 1:		Line 1:

	==Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit==		==Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit==
-	<StructureSection load='5tsk' size='340' side='right' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>	+	<StructureSection load='5tsk' size='340' side='right'caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TSK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TSK FirstGlance]. <br>
Line 10:		Line 10:
	</StructureSection>		</StructureSection>
	[[Category: Coxsackievirus a16]]		[[Category: Coxsackievirus a16]]
		+	[[Category: Large Structures]]
	[[Category: Cong, Y]]		[[Category: Cong, Y]]
	[[Category: Fan, C]]		[[Category: Fan, C]]

OCA at 18:09, 1 February 2017

OCA — Wed, 01 Feb 2017 18:09:41 GMT

←Older revision		Revision as of 18:09, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tsk is ~~ON HOLD until Paper Publication~~	+	==Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit==
-		+	<StructureSection load='5tsk' size='340' side='right' caption='[[5tsk]], [[Resolution\|resolution]] 6.50Å' scene=''>
-	~~Authors~~: ~~Fan~~, C., ~~Cong~~, Y., ~~Ye, X~~., ~~Huang, Z~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a16 Coxsackievirus a16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TSK FirstGlance]. <br>
-	~~Description~~: ~~Molecular Dynamics Flexible Fitting Model of~~ Coxsackievirus ~~A16 empty Procapsid VP1 Subunit~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tsl\|5tsl]]</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=5tsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tsk OCA], [http://pdbe.org/5tsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tsk RCSB], [http://www.ebi.ac.uk/pdbsum/5tsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tsk ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Coxsackievirus a16]]
		+	[[Category: Cong, Y]]
		+	[[Category: Fan, C]]
	[[Category: Huang, Z]]		[[Category: Huang, Z]]
-	[[Category: Cong, Y]]
	[[Category: Ye, X]]		[[Category: Ye, X]]
-	[[Category: ~~Fan, C~~]]	+	[[Category: Coxsackievirus]]
		+	[[Category: Virus]]

OCA at 21:18, 25 January 2017

OCA — Wed, 25 Jan 2017 21:18:04 GMT

←Older revision		Revision as of 21:18, 25 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Fan, C., Cong, Y., Ye, X., Huang, Z.		Authors: Fan, C., Cong, Y., Ye, X., Huang, Z.

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

OCA — Fri, 09 Dec 2016 17:48:44 GMT

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

←Older revision

Revision as of 17:48, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5tsk is ON HOLD Authors: Fan, C., Cong, Y., Ye, X., Huang, Z. Description: Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Pr...

OCA — Fri, 09 Dec 2016 17:48:43 GMT

New page: '''Unreleased structure''' The entry 5tsk is ON HOLD Authors: Fan, C., Cong, Y., Ye, X., Huang, Z. Description: Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Pr...

New page

'''Unreleased structure'''

The entry 5tsk is ON HOLD

Authors: Fan, C., Cong, Y., Ye, X., Huang, Z.

Description: Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit
[[Category: Unreleased Structures]]
[[Category: Huang, Z]]
[[Category: Cong, Y]]
[[Category: Ye, X]]
[[Category: Fan, C]]