4rs5 - Revision history

OCA at 12:55, 1 March 2024

2024-03-01T12:55:28Z

←Older revision		Revision as of 12:55, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterovirus_A71 Enterovirus A71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterovirus_A71 Enterovirus A71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>
-	</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [https://pdbe.org/4rs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [https://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 ProSAT]</span></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]] 3.805Å</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [https://pdbe.org/4rs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [https://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/F6KTB0_HE71 F6KTB0_HE71] 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]		[https://www.uniprot.org/uniprot/F6KTB0_HE71 F6KTB0_HE71] 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]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Hand-foot-and-mouth disease (HFMD) remains a major health concern in the Asia-Pacific regions, and its major causative agents include human enterovirus 71 (EV71) and coxsackievirus A16. A desirable vaccine against HFMD would be multivalent and able to elicit protective responses against multiple HFMD causative agents. Previously, we have demonstrated that a thermostable recombinant EV71 vaccine candidate can be produced by the insertion of a foreign peptide into the BC loop of VP1 without affecting viral replication. Here we present crystal structures of two different naturally occurring empty particles, one from a clinical C4 strain EV71 and the other from its recombinant virus containing an insertion in the VP1 BC loop. Crystal structure analysis demonstrated that the inserted foreign peptide is well exposed on the particle surface without significant structural changes in the capsid. Importantly, such insertions do not seem to affect the virus uncoating process as illustrated by the conformational similarity between an uncoating intermediate of another recombinant virus and that of EV71. Especially, at least 18 residues from the N terminus of VP1 are transiently externalized. Altogether, our study provides insights into vaccine development against HFMD.
-
-	Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design.,Lyu K, Wang GC, He YL, Han JF, Ye Q, Qin CF, Chen R J Biol Chem. 2015 Feb 6;290(6):3198-208. doi: 10.1074/jbc.M114.624536. Epub 2014 , Dec 9. PMID:25492868<ref>PMID:25492868</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rs5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]		*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:26, 8 March 2023

2023-03-08T08:26:41Z

←Older revision		Revision as of 08:26, 8 March 2023
Line 3:		Line 3:
	<StructureSection load='4rs5' size='340' side='right'caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>		<StructureSection load='4rs5' size='340' side='right'caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ev-71 Ev-71~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterovirus_A71 Enterovirus A71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</td></tr>~~	+	</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [https://pdbe.org/4rs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [https://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [~~http~~://pdbe.org/4rs5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F6KTB0_HE71 F6KTB0_HE71] 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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4rs5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4rs5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ev-71~~]]	+	[[Category: Enterovirus A71]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, R]]	+	[[Category: Chen R]]
-	[[Category: Lyu, K]]	+	[[Category: Lyu K]]
-	~~[[Category: Eight-stranded beta barrel]]~~	+
-	~~[[Category: Replicate in cytoplasm]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 09:39, 1 May 2019

2019-05-01T09:39:09Z

←Older revision		Revision as of 09:39, 1 May 2019
Line 1:		Line 1:

	==Crystal structure of an uncoating intermediate of a EV71 recombinant virus==		==Crystal structure of an uncoating intermediate of a EV71 recombinant virus==
-	<StructureSection load='4rs5' size='340' side='right' caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>	+	<StructureSection load='4rs5' size='340' side='right'caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Ev-71 Ev-71]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://pdbe.org/4rs5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://pdbe.org/4rs5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ev-71]]
		+	[[Category: Large Structures]]
	[[Category: Chen, R]]		[[Category: Chen, R]]
	[[Category: Lyu, K]]		[[Category: Lyu, K]]

OCA at 17:18, 18 January 2017

2017-01-18T17:18:56Z

←Older revision		Revision as of 17:18, 18 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of an uncoating intermediate of a EV71 recombinant virus==		==Crystal structure of an uncoating intermediate of a EV71 recombinant virus==
	<StructureSection load='4rs5' size='340' side='right' caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>		<StructureSection load='4rs5' size='340' side='right' caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum]</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://pdbe.org/4rs5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rs5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4rs5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:28, 15 April 2015

2015-04-15T06:28:34Z

←Older revision		Revision as of 06:28, 15 April 2015
Line 6:		Line 6:
	<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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum]</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hand-foot-and-mouth disease (HFMD) remains a major health concern in the Asia-Pacific regions, and its major causative agents include human enterovirus 71 (EV71) and coxsackievirus A16. A desirable vaccine against HFMD would be multivalent and able to elicit protective responses against multiple HFMD causative agents. Previously, we have demonstrated that a thermostable recombinant EV71 vaccine candidate can be produced by the insertion of a foreign peptide into the BC loop of VP1 without affecting viral replication. Here we present crystal structures of two different naturally occurring empty particles, one from a clinical C4 strain EV71 and the other from its recombinant virus containing an insertion in the VP1 BC loop. Crystal structure analysis demonstrated that the inserted foreign peptide is well exposed on the particle surface without significant structural changes in the capsid. Importantly, such insertions do not seem to affect the virus uncoating process as illustrated by the conformational similarity between an uncoating intermediate of another recombinant virus and that of EV71. Especially, at least 18 residues from the N terminus of VP1 are transiently externalized. Altogether, our study provides insights into vaccine development against HFMD.
		+
		+	Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design.,Lyu K, Wang GC, He YL, Han JF, Ye Q, Qin CF, Chen R J Biol Chem. 2015 Feb 6;290(6):3198-208. doi: 10.1074/jbc.M114.624536. Epub 2014 , Dec 9. PMID:25492868<ref>PMID:25492868</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:00, 17 December 2014

2014-12-17T13:00:57Z

←Older revision		Revision as of 13:00, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of an uncoating intermediate of a EV71 recombinant virus==
-		+	<StructureSection load='4rs5' size='340' side='right' caption='[[4rs5]], [[Resolution\|resolution]] 3.81Å' scene=''>
-	~~The entry~~ 4rs5 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4rs5]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RS5 FirstGlance]. <br>
-	~~Authors~~: ~~Chen~~, R., Lyu, K.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n43\|4n43]], [[4n53\|4n53]], [[4rqp\|4rqp]], [[4rr3\|4rr3]]</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=4rs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rs5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rs5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rs5 PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of an uncoating intermediate of a EV71 recombinant virus~~	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, R]]
		+	[[Category: Lyu, K]]
		+	[[Category: Eight-stranded beta barrel]]
		+	[[Category: Replicate in cytoplasm]]
		+	[[Category: Virus]]

OCA: Protected "4rs5" [edit=sysop:move=sysop]

2014-11-19T11:32:36Z

Protected "4rs5" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:32, 19 November 2014

OCA: New page: '''Unreleased structure''' The entry 4rs5 is ON HOLD Authors: Chen, R., Lyu, K. Description: Crystal structure of an uncoating intermediate of a EV71 recombinant virus

2014-11-19T11:32:35Z

New page: '''Unreleased structure''' The entry 4rs5 is ON HOLD Authors: Chen, R., Lyu, K. Description: Crystal structure of an uncoating intermediate of a EV71 recombinant virus

New page

'''Unreleased structure'''

The entry 4rs5 is ON HOLD

Authors: Chen, R., Lyu, K.

Description: Crystal structure of an uncoating intermediate of a EV71 recombinant virus