1ev1 - Revision history

OCA at 10:06, 20 March 2024

OCA — Wed, 20 Mar 2024 10:06:43 GMT

←Older revision		Revision as of 10:06, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='1ev1' size='340' side='right'caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='1ev1' size='340' side='right'caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human_echovirus_1 Human echovirus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Echovirus_E1 Echovirus E1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.55Å</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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [https://pdbe.org/1ev1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ev1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [https://pdbe.org/1ev1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ev1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ev1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_EC01F POLG_EC01F]] 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 integrin ITGA2/ITGB1 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref>	+	[https://www.uniprot.org/uniprot/POLG_EC01F POLG_EC01F] 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 integrin ITGA2/ITGB1 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref>
	== 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=1ev1 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=1ev1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.
-
-	Structure determination of echovirus 1.,Filman DJ, Wien MW, Cunningham JA, Bergelson JM, Hogle JM Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1261-72. PMID:10089503<ref>PMID:10089503</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ev1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human echovirus 1~~]]	+	[[Category: Echovirus E1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Filman~~, D J~~]]	+	[[Category: Filman DJ]]
-	[[Category: Hogle~~, J M~~]]	+	[[Category: Hogle JM]]
-	[[Category: Wien~~, M W]]~~	+	[[Category: Wien MW]]
-	~~[[Category: Capsid]]~~	+
-	~~[[Category: Echovirus]]~~	+
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Picornavirus]]~~	+
-	~~[[Category: Viral coat protein]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 09:42, 21 July 2021

OCA — Wed, 21 Jul 2021 09:42:15 GMT

←Older revision		Revision as of 09:42, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1ev1' size='340' side='right'caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='1ev1' size='340' side='right'caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human_echovirus_1 Human echovirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_echovirus_1 Human echovirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [~~http~~://pdbe.org/1ev1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ev1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [https://pdbe.org/1ev1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ev1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ev1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_EC01F POLG_EC01F]] 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 integrin ITGA2/ITGB1 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref>	+	[[https://www.uniprot.org/uniprot/POLG_EC01F POLG_EC01F]] 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 integrin ITGA2/ITGB1 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref>
	== 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 1ev1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ev1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:50, 16 October 2019

OCA — Wed, 16 Oct 2019 08:50:59 GMT

←Older revision		Revision as of 08:50, 16 October 2019
Line 1:		Line 1:

	==ECHOVIRUS 1==		==ECHOVIRUS 1==
-	<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>	+	<StructureSection load='1ev1' size='340' side='right'caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_echovirus_1 Human echovirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_echovirus_1 Human echovirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Human echovirus 1]]		[[Category: Human echovirus 1]]
		+	[[Category: Large Structures]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 07:06, 20 December 2017

OCA — Wed, 20 Dec 2017 07:06:51 GMT

←Older revision		Revision as of 07:06, 20 December 2017
Line 1:		Line 1:
		+
	==ECHOVIRUS 1==		==ECHOVIRUS 1==
	<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~E-1 E-~~1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_echovirus_1 Human echovirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://pdbe.org/1ev1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://pdbe.org/1ev1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ev1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ev/1ev1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ev/1ev1_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 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: E-1]]	+	[[Category: Human echovirus 1]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 10:41, 9 February 2016

OCA — Tue, 09 Feb 2016 10:41:34 GMT

←Older revision		Revision as of 10:41, 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=1ev1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:29, 10 September 2015

OCA — Thu, 10 Sep 2015 21:29:37 GMT

←Older revision		Revision as of 21:29, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>		<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Echovirus_e1 Echovirus e1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/E-1 E-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://pdbe.org/1ev1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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 1ev1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Echovirus e1~~]]	+	[[Category: E-1]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 06:20, 25 December 2014

OCA — Thu, 25 Dec 2014 06:20:09 GMT

←Older revision		Revision as of 06:20, 25 December 2014
Line 6:		Line 6:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_EC01F POLG_EC01F]] 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 integrin ITGA2/ITGB1 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> Protease 3C: cleaves host DDX58/RIG-I and thus contributes to the inhibition of type I interferon production. Cleaves also host PABPC1 (By similarity).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref> 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).<ref>PMID:11799180</ref> <ref>PMID:15356270</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 00:09, 23 December 2014

OCA — Tue, 23 Dec 2014 00:09:31 GMT

←Older revision		Revision as of 00:09, 23 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echovirus_e1 Echovirus e1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echovirus_e1 Echovirus e1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Echovirus e1]]		[[Category: Echovirus e1]]
-	[[Category: Filman, D J.]]	+	[[Category: Filman, D J]]
-	[[Category: Hogle, J M.]]	+	[[Category: Hogle, J M]]
-	[[Category: Wien, M W.]]	+	[[Category: Wien, M W]]
	[[Category: Capsid]]		[[Category: Capsid]]
	[[Category: Echovirus]]		[[Category: Echovirus]]

OCA at 11:16, 24 September 2014

OCA — Wed, 24 Sep 2014 11:16:37 GMT

←Older revision		Revision as of 11:16, 24 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ev1.~~png\|left~~\|200px]]	+	==ECHOVIRUS 1==
		+	<StructureSection load='1ev1' size='340' side='right' caption='[[1ev1]], [[Resolution\|resolution]] 3.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ev1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Echovirus_e1 Echovirus e1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EV1 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=PLM:PALMITIC+ACID'>PLM</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=1ev1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ev1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ev1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ev1 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/ev/1ev1_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 ==
		+	The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.

-	~~{{STRUCTURE_1ev1\| PDB=1ev1 \| SCENE= }}~~	+	Structure determination of echovirus 1.,Filman DJ, Wien MW, Cunningham JA, Bergelson JM, Hogle JM Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1261-72. PMID:10089503<ref>PMID:10089503</ref>

-	~~===ECHOVIRUS 1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1ev1]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Echovirus_e1 Echovirus e1]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1EV1 OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010089503<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Echovirus e1]]		[[Category: Echovirus e1]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]

OCA: Protected "1ev1" [edit=sysop:move=sysop]

OCA — Wed, 14 Nov 2012 07:27:19 GMT

Protected "1ev1" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:27, 14 November 2012