1tme - Revision history

OCA at 08:40, 14 February 2024

OCA — Wed, 14 Feb 2024 08:40:31 GMT

←Older revision		Revision as of 08:40, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1tme' size='340' side='right'caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1tme' size='340' side='right'caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Murine_poliovirus_~~(~~strain_da~~) ~~Murine poliovirus~~ (~~strain da~~)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Theiler's_encephalomyelitis_virus_(STRAIN_DA) Theiler's encephalomyelitis virus (STRAIN DA)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TME FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [https://pdbe.org/1tme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [https://www.ebi.ac.uk/pdbsum/1tme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tme ProSAT]</span></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]] 2.8Å</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [https://pdbe.org/1tme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [https://www.ebi.ac.uk/pdbsum/1tme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tme ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_TMEVD POLG_TMEVD]] Leader protein: promotes host NUP98 phosphorylation and blocks the export of host mRNA from the nucleus. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. The leader protein also inhibit host interferon regulatory factor 3 (IRF3) dimerization, thereby blocking the transcriptional activation of IFN genes.<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> 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 (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protease 3C: 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 cooperatively to the protease (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2A: is involved in host translation shutoff. Nuclear localization is required for this function (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref>	+	[https://www.uniprot.org/uniprot/POLG_TMEVD POLG_TMEVD] Leader protein: promotes host NUP98 phosphorylation and blocks the export of host mRNA from the nucleus. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. The leader protein also inhibit host interferon regulatory factor 3 (IRF3) dimerization, thereby blocking the transcriptional activation of IFN genes.<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> 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 (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protease 3C: 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 cooperatively to the protease (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2A: is involved in host translation shutoff. Nuclear localization is required for this function (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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=1tme 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=1tme ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Theiler murine encephalomyelitis virus strains are categorized into two groups, a neurovirulent group that rapidly kills the host, and a demyelinating group that causes a generally nonlethal infection of motor neurons followed by a persistent infection of the white matter with demyelinating lesions similar to those found in multiple sclerosis. The three-dimensional structure of the DA strain, a member of the demyelinating group, has been determined at 2.8 A resolution. As in other picornaviruses, the icosahedral capsid is formed by the packing of wedge-shaped eight-stranded antiparallel beta barrels. The surface of Theiler virus has large star-shaped plateaus at the fivefold axes and broad depressions spanning the twofold axes. Several unusual structural features are clustered near one edge of the depression. These include two finger-like loops projecting from the surface (one formed by residues 78-85 of VP1, and the other formed by residues 56-65 of VP3) and a third loop containing three cysteines (residues 87, 89, and 91 of VP3), which appear to be covalently modified. Most of the sequence differences between the demyelinating and neurovirulent groups that could play a role in determining pathogenesis map to the surface of the star-shaped plateau. The distribution of these sequence differences on the surface of the virion is consistent with models in which the differences in the pathogenesis of the two groups of Theiler viruses are the result of differences in immunological or receptor-mediated recognition processes.
-
-	Three-dimensional structure of Theiler virus.,Grant RA, Filman DJ, Fujinami RS, Icenogle JP, Hogle JM Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2061-5. PMID:1549565<ref>PMID:1549565</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tme" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Filman~~, D J~~]]	+	[[Category: Filman DJ]]
-	[[Category: Grant~~, R A~~]]	+	[[Category: Grant RA]]
-	[[Category: Hogle~~, J M]]~~	+	[[Category: Hogle JM]]
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 09:29, 29 September 2021

OCA — Wed, 29 Sep 2021 09:29:28 GMT

←Older revision		Revision as of 09:29, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1tme' size='340' side='right'caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1tme' size='340' side='right'caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TME FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [~~http~~://pdbe.org/1tme PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tme PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tme ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [https://pdbe.org/1tme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [https://www.ebi.ac.uk/pdbsum/1tme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tme ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_TMEVD POLG_TMEVD]] Leader protein: promotes host NUP98 phosphorylation and blocks the export of host mRNA from the nucleus. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. The leader protein also inhibit host interferon regulatory factor 3 (IRF3) dimerization, thereby blocking the transcriptional activation of IFN genes.<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> 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 (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protease 3C: 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 cooperatively to the protease (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2A: is involved in host translation shutoff. Nuclear localization is required for this function (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref>	+	[[https://www.uniprot.org/uniprot/POLG_TMEVD POLG_TMEVD]] Leader protein: promotes host NUP98 phosphorylation and blocks the export of host mRNA from the nucleus. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. The leader protein also inhibit host interferon regulatory factor 3 (IRF3) dimerization, thereby blocking the transcriptional activation of IFN genes.<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> 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 (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protease 3C: 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 cooperatively to the protease (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2A: is involved in host translation shutoff. Nuclear localization is required for this function (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:19, 25 December 2019

OCA — Wed, 25 Dec 2019 14:19:16 GMT

←Older revision		Revision as of 14:19, 25 December 2019
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	==THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS==		==THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS==
-	<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1tme' size='340' side='right'caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>
Line 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Grant, R A]]		[[Category: Grant, R A]]

OCA at 09:06, 21 March 2018

OCA — Wed, 21 Mar 2018 09:06:41 GMT

←Older revision		Revision as of 09:06, 21 March 2018
Line 1:		Line 1:
		+
	==THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS==		==THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS==
	<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://pdbe.org/1tme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum]</span></td></tr>	+	</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://pdbe.org/1tme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tme ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tme_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tme_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>
	</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=1tme ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:14, 11 September 2015

OCA — Fri, 11 Sep 2015 14:14:17 GMT

←Older revision		Revision as of 14:14, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tme]] 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=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tme]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Murine_poliovirus_(strain_da) Murine poliovirus (strain da)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum]</span></td></tr>	+	</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://pdbe.org/1tme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	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 1tme" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Viruses]]
	[[Category: Filman, D J]]		[[Category: Filman, D J]]
	[[Category: Grant, R A]]		[[Category: Grant, R A]]

OCA at 17:33, 25 December 2014

OCA — Thu, 25 Dec 2014 17:33:44 GMT

←Older revision		Revision as of 17:33, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tme]] 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=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tme]] 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=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>
-	</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum]</span></td></tr>	+	</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLG_TMEVD POLG_TMEVD]] Leader protein: promotes host NUP98 phosphorylation and blocks the export of host mRNA from the nucleus. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. The leader protein also inhibit host interferon regulatory factor 3 (IRF3) dimerization, thereby blocking the transcriptional activation of IFN genes.<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> 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 (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protease 3C: 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 cooperatively to the protease (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref> Protein 2A: is involved in host translation shutoff. Nuclear localization is required for this function (By similarity).<ref>PMID:19088287</ref> <ref>PMID:19710133</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
-	[[Category: Filman, D J.]]	+	[[Category: Filman, D J]]
-	[[Category: Grant, R A.]]	+	[[Category: Grant, R A]]
-	[[Category: Hogle, J M.]]	+	[[Category: Hogle, J M]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Virus]]		[[Category: Virus]]

OCA at 20:44, 29 September 2014

OCA — Mon, 29 Sep 2014 20:44:52 GMT

←Older revision		Revision as of 20:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1tme.~~png\|left~~\|200px]]	+	==THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS==
		+	<StructureSection load='1tme' size='340' side='right' caption='[[1tme]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tme]] 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=1TME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TME FirstGlance]. <br>
		+	</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=1tme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tme RCSB], [http://www.ebi.ac.uk/pdbsum/1tme 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/tm/1tme_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 ==
		+	Theiler murine encephalomyelitis virus strains are categorized into two groups, a neurovirulent group that rapidly kills the host, and a demyelinating group that causes a generally nonlethal infection of motor neurons followed by a persistent infection of the white matter with demyelinating lesions similar to those found in multiple sclerosis. The three-dimensional structure of the DA strain, a member of the demyelinating group, has been determined at 2.8 A resolution. As in other picornaviruses, the icosahedral capsid is formed by the packing of wedge-shaped eight-stranded antiparallel beta barrels. The surface of Theiler virus has large star-shaped plateaus at the fivefold axes and broad depressions spanning the twofold axes. Several unusual structural features are clustered near one edge of the depression. These include two finger-like loops projecting from the surface (one formed by residues 78-85 of VP1, and the other formed by residues 56-65 of VP3) and a third loop containing three cysteines (residues 87, 89, and 91 of VP3), which appear to be covalently modified. Most of the sequence differences between the demyelinating and neurovirulent groups that could play a role in determining pathogenesis map to the surface of the star-shaped plateau. The distribution of these sequence differences on the surface of the virion is consistent with models in which the differences in the pathogenesis of the two groups of Theiler viruses are the result of differences in immunological or receptor-mediated recognition processes.

-	~~{{STRUCTURE_1tme\| PDB=1tme \| SCENE= }}~~	+	Three-dimensional structure of Theiler virus.,Grant RA, Filman DJ, Fujinami RS, Icenogle JP, Hogle JM Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2061-5. PMID:1549565<ref>PMID:1549565</ref>

-	~~===THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1549565}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1tme]] 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=1TME OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:001549565<~~/~~ref~~><~~ref group="xtra">PMID:019756040</ref><references group="xtra"~~/>	+
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]

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

OCA — Sat, 05 Jan 2013 11:35:56 GMT

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

←Older revision

Revision as of 11:35, 5 January 2013

OCA at 11:35, 5 January 2013

OCA — Sat, 05 Jan 2013 11:35:52 GMT

←Older revision		Revision as of 11:35, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1tme.png\|left\|200px]]		[[Image:1tme.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1tme", 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_1tme\| PDB=1tme \| SCENE= }}		{{STRUCTURE_1tme\| PDB=1tme \| SCENE= }}

	===THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS===		===THREE-DIMENSIONAL STRUCTURE OF THEILER VIRUS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1549565}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1549565 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1549565}}		{{ABSTRACT_PUBMED_1549565}}

	==About this Structure==		==About this Structure==
-	~~1TME~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Theiler's_murine_encephalomyelitis_virus Theiler's murine encephalomyelitis virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA].	+	[[1tme]] 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=1TME OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~1549565~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:001549565</ref><ref group="xtra">PMID:019756040</ref><references group="xtra"/>
-	[[Category: ~~Theiler's murine encephalomyelitis virus~~]]	+	[[Category: Viruses]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]
	[[Category: Grant, R A.]]		[[Category: Grant, R A.]]
Line 30:		Line 18:
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]
	[[Category: Virus]]		[[Category: Virus]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:20:21 2009''

OCA at 22:20, 17 February 2009

OCA — Tue, 17 Feb 2009 22:20:24 GMT

←Older revision		Revision as of 22:20, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1TME is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Theiler's_murine_encephalomyelitis_virus Theiler's murine encephalomyelitis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA].	+	1TME is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Theiler's_murine_encephalomyelitis_virus Theiler's murine encephalomyelitis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TME OCA].

	==Reference==		==Reference==
-	~~Three-dimensional structure of Theiler virus., Grant RA, Filman DJ, Fujinami RS, Icenogle JP, Hogle JM, Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2061-5.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/1549565 1549565]~~	+	<ref group="xtra">PMID:1549565</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Theiler's murine encephalomyelitis virus]]		[[Category: Theiler's murine encephalomyelitis virus]]
	[[Category: Filman, D J.]]		[[Category: Filman, D J.]]
Line 32:		Line 31:
	[[Category: Virus]]		[[Category: Virus]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:42:~~06 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:20:21 2009''