1oop - Revision history

OCA at 06:09, 3 April 2024

2024-04-03T06:09:39Z

← Older revision		Revision as of 06:09, 3 April 2024
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oop ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oop ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

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

OCA at 08:02, 14 February 2024

2024-02-14T08:02:09Z

← Older revision		Revision as of 08:02, 14 February 2024
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	<StructureSection load='1oop' size='340' side='right'caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1oop' size='340' side='right'caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Svdv Svdv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Swine_vesicular_disease_virus_(STRAIN_UKG/27/72) Swine vesicular disease virus (STRAIN UKG/27/72)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [https://pdbe.org/1oop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [https://www.ebi.ac.uk/pdbsum/1oop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oop 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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [https://pdbe.org/1oop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [https://www.ebi.ac.uk/pdbsum/1oop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oop ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/POLG_SVDVU POLG_SVDVU]] 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 CXADR 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity). 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 (By similarity).		[https://www.uniprot.org/uniprot/POLG_SVDVU POLG_SVDVU] 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 CXADR 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity). 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oop ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oop ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-A crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.

	Crystal structure of Swine vesicular disease virus and implications for host adaptation.,Fry EE, Knowles NJ, Newman JW, Wilsden G, Rao Z, King AM, Stuart DI J Virol. 2003 May;77(9):5475-86. PMID:12692248<ref>PMID:12692248</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1oop" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Svdv]]~~		[[Category: Fry EE]]
	[[Category: Fry~~, E E~~]]		[[Category: King AMQ]]
	[[Category: King~~, A M.Q~~]]		[[Category: Knowles NJ]]
	[[Category: Knowles~~, N J~~]]		[[Category: Newman JWI]]
	[[Category: Newman~~, J W.I~~]]		[[Category: Rao Z]]
	[[Category: Rao, Z]]		[[Category: Stuart DI]]
	[[Category: Stuart~~, D I~~]]		[[Category: Wilsden G]]
	[[Category: Wilsden, G]]
	~~[[Category: Car]]~~
	~~[[Category: Coxsackievirus]]~~
	~~[[Category: Daf]]~~
	~~[[Category: Host adaptation]]~~
	~~[[Category: Icosahedral virus]]~~
	~~[[Category: Picornavirus structure]]~~
	~~[[Category: Virus]]~~
	~~[[Category: Virus-receptor interaction]]~~
	~~[[Category: Virus/viral protein~~]]

OCA at 08:58, 21 April 2021

2021-04-21T08:58:03Z

← Older revision		Revision as of 08:58, 21 April 2021
Line 3:		Line 3:
	<StructureSection load='1oop' size='340' side='right'caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1oop' size='340' side='right'caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Svdv Svdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Svdv Svdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [~~http~~://pdbe.org/1oop PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1oop PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1oop 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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [https://pdbe.org/1oop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [https://www.ebi.ac.uk/pdbsum/1oop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oop ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/POLG_SVDVU POLG_SVDVU]] 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 CXADR 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity). 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 (By similarity).		[[https://www.uniprot.org/uniprot/POLG_SVDVU POLG_SVDVU]] 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 CXADR 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity). 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1oop" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1oop" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[User:Eric Martz/Entertaining PDB codes\|User:Eric Martz/Entertaining PDB codes]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:05, 17 July 2019

2019-07-17T13:05:28Z

← Older revision		Revision as of 13:05, 17 July 2019
Line 1:		Line 1:

	==The Crystal Structure of Swine Vesicular Disease Virus==		==The Crystal Structure of Swine Vesicular Disease Virus==
	<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1oop' size='340' side='right'caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Svdv Svdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Svdv Svdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/1oop_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/1oop_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Svdv]]		[[Category: Svdv]]
	[[Category: Fry, E E]]		[[Category: Fry, E E]]

OCA at 08:16, 12 October 2017

2017-10-12T08:16:05Z

← Older revision		Revision as of 08:16, 12 October 2017
Line 1:		Line 1:

	==The Crystal Structure of Swine Vesicular Disease Virus==		==The Crystal Structure of Swine Vesicular Disease Virus==
	<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Swine_vesicular_disease_virus_(strain_ukg/27/72) Swine vesicular disease virus (strain ukg/27/72)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Svdv Svdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://pdbe.org/1oop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop 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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://pdbe.org/1oop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oop ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1oop" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1oop" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[User:Eric Martz/Entertaining PDB codes\|User:Eric Martz/Entertaining PDB codes]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Svdv]]
	[[Category: Fry, E E]]		[[Category: Fry, E E]]
	[[Category: King, A M.Q]]		[[Category: King, A M.Q]]

OCA at 12:49, 9 February 2016

2016-02-09T12:49:29Z

← Older revision		Revision as of 12:49, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oop ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:24, 10 September 2015

2015-09-10T22:24:55Z

← Older revision		Revision as of 22:24, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Viruses Viruses~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Swine_vesicular_disease_virus_(strain_ukg/27/72) Swine vesicular disease virus (strain ukg/27/72)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop 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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://pdbe.org/1oop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1oop" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Viruses]]~~
	[[Category: Fry, E E]]		[[Category: Fry, E E]]
	[[Category: King, A M.Q]]		[[Category: King, A M.Q]]

OCA at 06:56, 25 December 2014

2014-12-25T06:56:01Z

← Older revision		Revision as of 06:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop 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=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/POLG_SVDVU POLG_SVDVU]] 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 CXADR 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 cyctoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity). 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 (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Fry, E E.]]		[[Category: Fry, E E]]
	[[Category: King, A M.Q.]]		[[Category: King, A M.Q]]
	[[Category: Knowles, N J.]]		[[Category: Knowles, N J]]
	[[Category: Newman, J W.I.]]		[[Category: Newman, J W.I]]
	[[Category: Rao, Z.]]		[[Category: Rao, Z]]
	[[Category: Stuart, D I.]]		[[Category: Stuart, D I]]
	[[Category: Wilsden, G.]]		[[Category: Wilsden, G]]
	[[Category: Car]]		[[Category: Car]]
	[[Category: Coxsackievirus]]		[[Category: Coxsackievirus]]

OCA at 13:08, 28 September 2014

2014-09-28T13:08:56Z

← Older revision		Revision as of 13:08, 28 September 2014
Line 1:		Line 1:
	[[Image:~~1oop~~.~~png~~\|~~left~~\|~~200px~~]]		==The Crystal Structure of Swine Vesicular Disease Virus==
			<StructureSection load='1oop' size='340' side='right' caption='[[1oop]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1oop]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OOP FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene>, <scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene><br>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oop RCSB], [http://www.ebi.ac.uk/pdbsum/1oop PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/1oop_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-A crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.

	~~{{STRUCTURE_1oop\| PDB=1oop \| SCENE= }}~~		Crystal structure of Swine vesicular disease virus and implications for host adaptation.,Fry EE, Knowles NJ, Newman JW, Wilsden G, Rao Z, King AM, Stuart DI J Virol. 2003 May;77(9):5475-86. PMID:12692248<ref>PMID:12692248</ref>

	~~===The Crystal Structure~~ of ~~Swine Vesicular Disease Virus===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_12692248}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1oop]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Viruses Viruses]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1OOP OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:012692248<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Fry, E E.]]		[[Category: Fry, E E.]]

OCA: Protected "1oop" [edit=sysop:move=sysop]

2012-12-12T21:51:48Z

Protected "1oop" [edit=sysop:move=sysop]

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