1pvc - Revision history

OCA at 05:59, 17 April 2024

OCA — Wed, 17 Apr 2024 05:59:40 GMT

←Older revision		Revision as of 05:59, 17 April 2024
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	<StructureSection load='1pvc' size='340' side='right'caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1pvc' size='340' side='right'caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Poliovirus_type_3_(~~strains_p3~~/~~leon~~/~~37_and_p3~~/~~leon_12a[1]b~~) Poliovirus type 3 (strains p3/~~leon~~/37 ~~and p3~~/~~leon 12a[1]b~~)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pvc]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_P3/LEON/37_AND_P3/LEON_12A1B) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A1B)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVC 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]] 2.4Å</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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [https://pdbe.org/1pvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [https://www.ebi.ac.uk/pdbsum/1pvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvc 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [https://pdbe.org/1pvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [https://www.ebi.ac.uk/pdbsum/1pvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_POL3L POLG_POL3L]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).	+	[https://www.uniprot.org/uniprot/POLG_POL3L POLG_POL3L] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Filman~~, D J~~]]	+	[[Category: Filman DJ]]
-	[[Category: Hogle~~, J M~~]]	+	[[Category: Hogle JM]]
-	[[Category: Syed, R]]	+	[[Category: Syed R]]
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 09:35, 8 September 2021

OCA — Wed, 08 Sep 2021 09:35:24 GMT

←Older revision		Revision as of 09:35, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1pvc' size='340' side='right'caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1pvc' size='340' side='right'caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVC 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [~~http~~://pdbe.org/1pvc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pvc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvc 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [https://pdbe.org/1pvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [https://www.ebi.ac.uk/pdbsum/1pvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_POL3L POLG_POL3L]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).	+	[[https://www.uniprot.org/uniprot/POLG_POL3L POLG_POL3L]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1pvc 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=1pvc 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 10:07, 27 November 2019

OCA — Wed, 27 Nov 2019 10:07:39 GMT

←Older revision		Revision as of 10:07, 27 November 2019
Line 1:		Line 1:

	==REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION==		==REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION==
-	<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1pvc' size='340' side='right'caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 08:08, 24 February 2018

OCA — Sat, 24 Feb 2018 08:08:41 GMT

←Older revision		Revision as of 08:08, 24 February 2018
Line 1:		Line 1:
		+
	==REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION==		==REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION==
	<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://pdbe.org/1pvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://pdbe.org/1pvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvc 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/pv/1pvc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/1pvc_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>

OCA at 21:48, 8 February 2016

OCA — Mon, 08 Feb 2016 21:48:38 GMT

←Older revision		Revision as of 21:48, 8 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=1pvc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	__TOC__		__TOC__

OCA at 15:42, 10 September 2015

OCA — Thu, 10 Sep 2015 15:42:00 GMT

←Older revision		Revision as of 15:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pvc]] 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=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pvc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Poliovirus_type_3_(strains_p3/leon/37_and_p3/leon_12a[1]b) Poliovirus type 3 (strains p3/leon/37 and p3/leon 12a[1]b)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://pdbe.org/1pvc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Viruses]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 02:22, 25 December 2014

OCA — Thu, 25 Dec 2014 02:22:10 GMT

←Older revision		Revision as of 02:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pvc]] 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=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pvc]] 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=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc 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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_POL3L POLG_POL3L]] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm (By similarity). VP0 precursor is a component of immature procapsids (By similarity). Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity). Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
-	[[Category: Filman, D J.]]	+	[[Category: Filman, D J]]
-	[[Category: Hogle, J M.]]	+	[[Category: Hogle, J M]]
-	[[Category: Syed, R.]]	+	[[Category: Syed, R]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 23:54, 28 September 2014

OCA — Sun, 28 Sep 2014 23:54:56 GMT

←Older revision		Revision as of 23:54, 28 September 2014
Line 1:		Line 1:
-	~~[[Image:1pvc.png\|left\|200px]]~~	+	==REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION==
-		+	<StructureSection load='1pvc' size='340' side='right' caption='[[1pvc]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{STRUCTURE_1pvc\| PDB=1pvc \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1pvc]] 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=1PVC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVC FirstGlance]. <br>
-	===REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION===	+	</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=1pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pvc RCSB], [http://www.ebi.ac.uk/pdbsum/1pvc PDBsum]</span></td></tr>
-	~~{{ABSTRACT_PUBMED_011159387}}~~	+	<table>
-		+	== Evolutionary Conservation ==
-	==~~About this Structure~~==	+	[[Image:Consurf_key_small.gif\|200px\|right]]
-	[[1pvc]] 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=1PVC OCA].	+	Check<jmol>
-		+	<jmolCheckbox>
-	==~~Reference~~==	+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/1pvc_consurf.spt"</scriptWhenChecked>
-	<~~ref group~~="~~xtra~~">~~PMID~~:~~011159387~~</~~ref~~><~~references group~~="~~xtra~~"/>	+	<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>
		+	__TOC__
		+	</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]

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

OCA — Wed, 19 Dec 2012 12:10:20 GMT

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

←Older revision

Revision as of 12:10, 19 December 2012

OCA at 12:10, 19 December 2012

OCA — Wed, 19 Dec 2012 12:10:17 GMT

←Older revision		Revision as of 12:10, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pvc.png\|left\|200px]]		[[Image:1pvc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pvc", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1pvc\| PDB=1pvc \| SCENE= }}		{{STRUCTURE_1pvc\| PDB=1pvc \| SCENE= }}

	===REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION===		===REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION===

		+	{{ABSTRACT_PUBMED_011159387}}

	==About this Structure==		==About this Structure==
-	~~1PVC~~ is a ~~5 chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Human_poliovirus Human poliovirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVC OCA].	+	[[1pvc]] 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=1PVC OCA].
-	[[Category: ~~Human poliovirus~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:011159387</ref><references group="xtra"/>
		+	[[Category: Viruses]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]
	[[Category: Hogle, J M.]]		[[Category: Hogle, J M.]]
Line 21:		Line 18:
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Virus]]		[[Category: Virus]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:45:05 2009''