3jbg - Revision history

OCA at 10:00, 21 December 2022

2022-12-21T10:00:35Z

←Older revision		Revision as of 10:00, 21 December 2022
Line 3:		Line 3:
	<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arabian_camel Arabian camel~~] and [https://en.wikipedia.org/wiki/~~Human_poliovirus_1_mahoney~~ Human poliovirus 1 ~~mahoney~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [https://en.wikipedia.org/wiki/Human_poliovirus_1_Mahoney Human poliovirus 1 Mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MYR~~:~~MYRISTIC~~+ACID'>~~MYR~~</scene~~></td></tr>~~	+
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</div></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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [https://pdbe.org/3jbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [https://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg 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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [https://pdbe.org/3jbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [https://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M]] 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>	+	[https://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M] 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Arabian camel~~]]	+	[[Category: Camelus dromedarius]]
-	[[Category: Human poliovirus 1 ~~mahoney~~]]	+	[[Category: Human poliovirus 1 Mahoney]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Filman~~, D J~~]]	+	[[Category: Filman DJ]]
-	[[Category: Hogle~~, J M~~]]	+	[[Category: Hogle JM]]
-	[[Category: Schotte, L]]	+	[[Category: Schotte L]]
-	[[Category: Strauss, M]]	+	[[Category: Strauss M]]
-	[[Category: Thys, B]]	+	[[Category: Thys B]]
-	~~[[Category: Nanobody]]~~	+
-	~~[[Category: Neutralizing antibody]]~~	+
-	~~[[Category: Poliovirus]]~~	+
-	~~[[Category: Vhh]]~~	+
-	~~[[Category: Virus-immune system complex~~]]	+

OCA at 13:31, 4 May 2022

2022-05-04T13:31:06Z

←Older revision		Revision as of 13:31, 4 May 2022
Line 3:		Line 3:
	<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [~~http~~://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3JBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [https://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [~~http~~://pdbe.org/3jbg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg 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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [https://pdbe.org/3jbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [https://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M]] 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>	+	[[https://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M]] 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3jbg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3jbg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:26, 10 April 2020

2020-04-10T18:26:56Z

←Older revision		Revision as of 18:26, 10 April 2020
Line 3:		Line 3:
	<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3JBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [http://pdbe.org/3jbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [http://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [http://pdbe.org/3jbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [http://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:37, 6 March 2020

2020-03-06T17:37:53Z

←Older revision		Revision as of 17:37, 6 March 2020
Line 1:		Line 1:

	==Complex of poliovirus with VHH PVSS21E==		==Complex of poliovirus with VHH PVSS21E==
-	<~~StructureSection~~ load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='3jbg' size='340' side='right' viewer='molstar' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
Line 23:		Line 23:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Arabian camel]]		[[Category: Arabian camel]]
	[[Category: Human poliovirus 1 mahoney]]		[[Category: Human poliovirus 1 mahoney]]
		+	[[Category: Large Structures]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Hogle, J M]]		[[Category: Hogle, J M]]

OCA at 08:26, 18 July 2018

2018-07-18T08:26:51Z

←Older revision		Revision as of 08:26, 18 July 2018
Line 3:		Line 3:
	<StructureSection load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [http://pdbe.org/3jbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [http://www.ebi.ac.uk/pdbsum/3jbg 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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [http://pdbe.org/3jbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [http://www.ebi.ac.uk/pdbsum/3jbg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arabian camel]]
	[[Category: Human poliovirus 1 mahoney]]		[[Category: Human poliovirus 1 mahoney]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]

OCA at 16:06, 10 May 2016

2016-05-10T16:06:37Z

←Older revision		Revision as of 16:06, 10 May 2016
Line 1:		Line 1:
		+
	==Complex of poliovirus with VHH PVSS21E==		==Complex of poliovirus with VHH PVSS21E==
	<StructureSection load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>

OCA at 02:11, 28 January 2016

2016-01-28T02:11:11Z

←Older revision		Revision as of 02:11, 28 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Complex of poliovirus with VHH PVSS21E==
		+	<StructureSection load='3jbg' size='340' side='right' caption='[[3jbg]], [[Resolution\|resolution]] 3.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3jbg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human_poliovirus_1_mahoney Human poliovirus 1 mahoney]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYR:MYRISTIC+ACID'>MYR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3jbc\|3jbc]], [[3jbd\|3jbd]], [[3jbe\|3jbe]], [[3jbf\|3jbf]]</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=3jbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbg OCA], [http://pdbe.org/3jbg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbg RCSB], [http://www.ebi.ac.uk/pdbsum/3jbg PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M]] 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> 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).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nanobodies(R), or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five the VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. IMPORTANCE: We describe the cryo-EM structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8-6.3A. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the similarity of the binding surface on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of, but smaller in magnitude than, changes associated with cell entry, suggesting that this VHH has trapped the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed.

-	~~The entry 3jbg is ON HOLD until Paper Publication~~	+	Five of five VHHs neutralizing poliovirus bind the receptor-binding site.,Strauss M, Schotte L, Thys B, Filman DJ, Hogle JM J Virol. 2016 Jan 13. pii: JVI.03017-15. PMID:26764003<ref>PMID:26764003</ref>

-	~~Authors: Strauss~~, M.~~, Schotte, L~~.~~, Thys, B., Filman, D.J., Hogle, J.M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Complex of~~ poliovirus ~~with VHH PVSS21E~~	+	<div class="pdbe-citations 3jbg" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human poliovirus 1 mahoney]]
		+	[[Category: Filman, D J]]
		+	[[Category: Hogle, J M]]
	[[Category: Schotte, L]]		[[Category: Schotte, L]]
		+	[[Category: Strauss, M]]
	[[Category: Thys, B]]		[[Category: Thys, B]]
-	[[Category: ~~Hogle, J.M~~]]	+	[[Category: Nanobody]]
-	[[Category: ~~Filman, D.J~~]]	+	[[Category: Neutralizing antibody]]
-	[[Category: ~~Strauss, M~~]]	+	[[Category: Poliovirus]]
		+	[[Category: Vhh]]
		+	[[Category: Virus-immune system complex]]

OCA at 08:37, 30 September 2015

2015-09-30T08:37:31Z

←Older revision		Revision as of 08:37, 30 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3jbg is ON HOLD	+	The entry 3jbg is ON HOLD until Paper Publication

-	Authors: Strauss M, Schotte L, Thys B, Filman DJ, Hogle JM	+	Authors: Strauss, M., Schotte, L., Thys, B., Filman, D.J., Hogle, J.M.

-	Description: ~~complex~~ of poliovirus with VHH PVSS21E	+	Description: Complex of poliovirus with VHH PVSS21E
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Strauss M,~~ Schotte L, Thys B, Filman Dj, ~~Hogle Jm~~]]	+	[[Category: Schotte, L]]
		+	[[Category: Thys, B]]
		+	[[Category: Hogle, J.M]]
		+	[[Category: Filman, D.J]]
		+	[[Category: Strauss, M]]

OCA: Protected "3jbg" [edit=sysop:move=sysop]

2015-09-02T07:02:00Z

Protected "3jbg" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:02, 2 September 2015

OCA: New page: '''Unreleased structure''' The entry 3jbg is ON HOLD Authors: Strauss M, Schotte L, Thys B, Filman DJ, Hogle JM Description: complex of poliovirus with VHH PVSS21E [[Category: Unreleas...

2015-09-02T07:01:59Z

New page: '''Unreleased structure''' The entry 3jbg is ON HOLD Authors: Strauss M, Schotte L, Thys B, Filman DJ, Hogle JM Description: complex of poliovirus with VHH PVSS21E [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 3jbg is ON HOLD

Authors: Strauss M, Schotte L, Thys B, Filman DJ, Hogle JM

Description: complex of poliovirus with VHH PVSS21E
[[Category: Unreleased Structures]]
[[Category: Strauss M, Schotte L, Thys B, Filman Dj, Hogle Jm]]