6acz - Revision history

OCA at 19:26, 29 May 2024

OCA — Wed, 29 May 2024 19:26:10 GMT

←Older revision		Revision as of 19:26, 29 May 2024
Line 3:		Line 3:
	<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>		<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Coxsackievirus_a10~~ Coxsackievirus ~~a10~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_A10 Coxsackievirus A10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ACZ 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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [https://pdbe.org/6acz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [https://www.ebi.ac.uk/pdbsum/6acz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</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]] 4.3Å</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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [https://pdbe.org/6acz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [https://www.ebi.ac.uk/pdbsum/6acz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A1V0FT21_9ENTO A0A1V0FT21_9ENTO]] 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. After genome has been released, the channel shrinks.[RuleBase:RU364118] Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1.[RuleBase:RU364118] Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores.[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 dissassembly 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: Is 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. The 3C domain in the context of protein 3CD may have an RNA binding activity.[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. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.[RuleBase:RU364118]	+	[https://www.uniprot.org/uniprot/A0A1V0FT21_9ENTO A0A1V0FT21_9ENTO] 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. After genome has been released, the channel shrinks.[RuleBase:RU364118] Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1.[RuleBase:RU364118] Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores.[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 dissassembly 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: Is 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. The 3C domain in the context of protein 3CD may have an RNA binding activity.[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. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.[RuleBase:RU364118]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Coxsackievirus ~~a10~~]]	+	[[Category: Coxsackievirus A10]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cheng, T]]	+	[[Category: Cheng T]]
-	[[Category: Cui~~, Y X~~]]	+	[[Category: Cui YX]]
-	[[Category: Li~~, S W~~]]	+	[[Category: Li SW]]
-	[[Category: Xu~~, L F~~]]	+	[[Category: Xu LF]]
-	[[Category: Yan~~, X D~~]]	+	[[Category: Yan XD]]
-	[[Category: Zheng~~, Q B~~]]	+	[[Category: Zheng QB]]
-	[[Category: Zhou~~, Z H~~]]	+	[[Category: Zhou ZH]]
-	[[Category: Zhu, R]]	+	[[Category: Zhu R]]
-	~~[[Category: Cva10]]~~	+
-	~~[[Category: Immune complex]]~~	+
-	~~[[Category: Neutralizing antibody]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 11:37, 23 March 2022

OCA — Wed, 23 Mar 2022 11:37:13 GMT

←Older revision		Revision as of 11:37, 23 March 2022
Line 3:		Line 3:
	<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>		<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>
-	</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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [~~http~~://pdbe.org/6acz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6acz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [https://pdbe.org/6acz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [https://www.ebi.ac.uk/pdbsum/6acz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/A0A1V0FT21_9ENTO A0A1V0FT21_9ENTO]] 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. After genome has been released, the channel shrinks.[RuleBase:RU364118] Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1.[RuleBase:RU364118] Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores.[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 dissassembly 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: Is 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. The 3C domain in the context of protein 3CD may have an RNA binding activity.[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. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.[RuleBase:RU364118]	+	[[https://www.uniprot.org/uniprot/A0A1V0FT21_9ENTO A0A1V0FT21_9ENTO]] 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. After genome has been released, the channel shrinks.[RuleBase:RU364118] Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1.[RuleBase:RU364118] Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores.[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 dissassembly 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: Is 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. The 3C domain in the context of protein 3CD may have an RNA binding activity.[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. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.[RuleBase:RU364118]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6acz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6acz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:03, 10 April 2020

OCA — Fri, 10 Apr 2020 23:03:05 GMT

←Older revision		Revision as of 23:03, 10 April 2020
Line 3:		Line 3:
	<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>		<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>
-	</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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [http://pdbe.org/6acz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [http://www.ebi.ac.uk/pdbsum/6acz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></td></tr>	+	</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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [http://pdbe.org/6acz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [http://www.ebi.ac.uk/pdbsum/6acz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:22, 6 March 2020

OCA — Fri, 06 Mar 2020 20:22:36 GMT

←Older revision		Revision as of 20:22, 6 March 2020
Line 1:		Line 1:

	==The structure of CVA10 virus A-particle from its complex with Fab 2G8==		==The structure of CVA10 virus A-particle from its complex with Fab 2G8==
-	<~~StructureSection~~ load='6acz' size='340' side='right'caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>	+	<SX load='6acz' size='340' side='right' viewer='molstar' caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Coxsackievirus a10]]		[[Category: Coxsackievirus a10]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:41, 6 November 2019

OCA — Wed, 06 Nov 2019 07:41:11 GMT

←Older revision		Revision as of 07:41, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6acz is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The structure of CVA10 virus A-particle from its complex with Fab 2G8==
		+	<StructureSection load='6acz' size='340' side='right'caption='[[6acz]], [[Resolution\|resolution]] 4.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6acz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Coxsackievirus_a10 Coxsackievirus a10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ACZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ACZ FirstGlance]. <br>
		+	</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=6acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6acz OCA], [http://pdbe.org/6acz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6acz RCSB], [http://www.ebi.ac.uk/pdbsum/6acz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6acz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A1V0FT21_9ENTO A0A1V0FT21_9ENTO]] 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. After genome has been released, the channel shrinks.[RuleBase:RU364118] Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1.[RuleBase:RU364118] Protein 2A: Cysteine protease that cleaves viral polyprotein and specific host proteins. It is responsible for the cleavage between the P1 and P2 regions, first cleavage occurring in the polyprotein. Cleaves also the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA translation. Inhibits the host nucleus-cytoplasm protein and RNA trafficking by cleaving host members of the nuclear pores.[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 dissassembly 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: Is 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. The 3C domain in the context of protein 3CD may have an RNA binding activity.[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. VPg may be removed in the cytoplasm by an unknown enzyme termed "unlinkase". VPg is not cleaved off virion genomes because replicated genomic RNA are encapsidated at the site of replication.[RuleBase:RU364118]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Coxsackievirus A10 (CVA10) recently emerged as a major pathogen of hand, foot, and mouth disease and herpangina in children worldwide, and lack of a vaccine or a cure against CVA10 infections has made therapeutic antibody identification a public health priority. By targeting a local isolate, CVA10-FJ-01, we obtained a potent antibody, 2G8, against all three capsid forms of CVA10. We show that 2G8 exhibited both 100% preventive and 100% therapeutic efficacy against CVA10 infection in mice. Comparisons of the near-atomic cryo-electron microscopy structures of the three forms of CVA10 capsid and their complexes with 2G8 Fab reveal that a single Fab binds a border region across the three capsid proteins (VP1 to VP3) and explain 2G8's remarkable cross-reactivities against all three capsid forms. The atomic structures of this first neutralizing antibody of CVA10 should inform strategies for designing vaccines and therapeutics against CVA10 infections.

-	~~Authors:~~ Zhu, R~~., Zheng, Q.B.~~, Xu, L~~.F.~~, ~~Cui~~, Y~~.X.~~, Li, S~~.W.~~, ~~Yan~~, X.D., ~~Zhou~~, Z.H., ~~Cheng~~, T.	+	Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10.,Zhu R, Xu L, Zheng Q, Cui Y, Li S, He M, Yin Z, Liu D, Li S, Li Z, Chen Z, Yu H, Que Y, Liu C, Kong Z, Zhang J, Baker TS, Yan X, Hong Zhou Z, Cheng T, Xia N Sci Adv. 2018 Sep 19;4(9):eaat7459. doi: 10.1126/sciadv.aat7459. eCollection 2018, Sep. PMID:30255146<ref>PMID:30255146</ref>

-	~~Description: The structure~~ of ~~CVA10 virus A-particle from its complex with Fab 2G8~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Zhu, R~~]]	+	<div class="pdbe-citations 6acz" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Zhou, Z.H~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Coxsackievirus a10]]
		+	[[Category: Large Structures]]
	[[Category: Cheng, T]]		[[Category: Cheng, T]]
-	[[Category: Li, S.W]]	+	[[Category: Cui, Y X]]
-	[[Category: ~~Cui~~, ~~Y.X~~]]	+	[[Category: Li, S W]]
-	[[Category: Yan, X.D]]	+	[[Category: Xu, L F]]
-	[[Category: Xu, ~~L.F~~]]	+	[[Category: Yan, X D]]
-	[[Category: ~~Zheng~~, ~~Q.B~~]]	+	[[Category: Zheng, Q B]]
		+	[[Category: Zhou, Z H]]
		+	[[Category: Zhu, R]]
		+	[[Category: Cva10]]
		+	[[Category: Immune complex]]
		+	[[Category: Neutralizing antibody]]
		+	[[Category: Virus]]

OCA at 06:03, 26 September 2018

OCA — Wed, 26 Sep 2018 06:03:56 GMT

←Older revision		Revision as of 06:03, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T.		Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T.
Line 7:		Line 7:
	Description: The structure of CVA10 virus A-particle from its complex with Fab 2G8		Description: The structure of CVA10 virus A-particle from its complex with Fab 2G8
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Zhu, R]]
		+	[[Category: Zhou, Z.H]]
		+	[[Category: Cheng, T]]
	[[Category: Li, S.W]]		[[Category: Li, S.W]]
	[[Category: Cui, Y.X]]		[[Category: Cui, Y.X]]
-	[[Category: Zhu, R]]
	[[Category: Yan, X.D]]		[[Category: Yan, X.D]]
-	[[Category: Zhou, Z.H]]
	[[Category: Xu, L.F]]		[[Category: Xu, L.F]]
	[[Category: Zheng, Q.B]]		[[Category: Zheng, Q.B]]
-	[[Category: Cheng, T]]

OCA at 05:29, 29 August 2018

OCA — Wed, 29 Aug 2018 05:29:45 GMT

←Older revision		Revision as of 05:29, 29 August 2018
Line 5:		Line 5:
	Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T.		Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T.

-	Description: The structure of CVA10 virus A-particle in complex with Fab 2G8	+	Description: The structure of CVA10 virus A-particle from its complex with Fab 2G8
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Li, S.W]]		[[Category: Li, S.W]]

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

OCA — Thu, 09 Aug 2018 19:42:10 GMT

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

←Older revision

Revision as of 19:42, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6acz is ON HOLD Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T. Description: The structure of CVA10 ...

OCA — Thu, 09 Aug 2018 19:42:09 GMT

New page: '''Unreleased structure''' The entry 6acz is ON HOLD Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T. Description: The structure of CVA10 ...

New page

'''Unreleased structure'''

The entry 6acz is ON HOLD

Authors: Zhu, R., Zheng, Q.B., Xu, L.F., Cui, Y.X., Li, S.W., Yan, X.D., Zhou, Z.H., Cheng, T.

Description: The structure of CVA10 virus A-particle in complex with Fab 2G8
[[Category: Unreleased Structures]]
[[Category: Li, S.W]]
[[Category: Cui, Y.X]]
[[Category: Zhu, R]]
[[Category: Yan, X.D]]
[[Category: Zhou, Z.H]]
[[Category: Xu, L.F]]
[[Category: Zheng, Q.B]]
[[Category: Cheng, T]]