1vcq - Revision history

OCA at 13:24, 9 May 2024

2024-05-09T13:24:44Z

←Older revision		Revision as of 13:24, 9 May 2024
Line 3:		Line 3:
	<StructureSection load='1vcq' size='340' side='right'caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1vcq' size='340' side='right'caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Sfv Sfv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Semliki_Forest_virus Semliki Forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [https://pdbe.org/1vcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [https://www.ebi.ac.uk/pdbsum/1vcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcq 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]] 3.1Å</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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [https://pdbe.org/1vcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [https://www.ebi.ac.uk/pdbsum/1vcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLS_SFV POLS_SFV]] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> 6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>	+	[https://www.uniprot.org/uniprot/POLS_SFV POLS_SFV] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> 6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sfv~~]]	+	[[Category: Semliki Forest virus]]
-	[[Category: Choi, H K]]	+	[[Category: Choi H-K]]
-	[[Category: Lu, G]]	+	[[Category: Lu G]]
-	[[Category: Rossmann~~, M G]]~~	+	[[Category: Rossmann MG]]
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Nucleocapsid protein]]~~	+
-	~~[[Category: Polyprotein]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus coat protein~~]]	+

OCA at 13:20, 13 October 2021

2021-10-13T13:20:14Z

←Older revision		Revision as of 13:20, 13 October 2021
Line 3:		Line 3:
	<StructureSection load='1vcq' size='340' side='right'caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1vcq' size='340' side='right'caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [~~http~~://pdbe.org/1vcq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1vcq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcq 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [https://pdbe.org/1vcq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [https://www.ebi.ac.uk/pdbsum/1vcq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLS_SFV POLS_SFV]] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> 6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>	+	[[https://www.uniprot.org/uniprot/POLS_SFV POLS_SFV]] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> 6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:36, 8 January 2020

2020-01-08T10:36:04Z

←Older revision		Revision as of 10:36, 8 January 2020
Line 1:		Line 1:

	==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)==		==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)==
-	<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='1vcq' size='340' side='right'caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sfv]]		[[Category: Sfv]]
	[[Category: Choi, H K]]		[[Category: Choi, H K]]

OCA at 07:40, 4 April 2018

2018-04-04T07:40:36Z

←Older revision		Revision as of 07:40, 4 April 2018
Line 1:		Line 1:
		+
	==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)==		==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)==
	<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://pdbe.org/1vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://pdbe.org/1vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcq 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/vc/1vcq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/1vcq_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 01:16, 8 February 2016

2016-02-08T01:16:48Z

←Older revision		Revision as of 01:16, 8 February 2016
Line 15:		Line 15:
	<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=1vcq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:32, 10 September 2015

2015-09-10T06:32:00Z

←Older revision		Revision as of 06:32, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Semliki_forest_virus Semliki forest virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sfv Sfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://pdbe.org/1vcq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq 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 1vcq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Semliki forest virus~~]]	+	[[Category: Sfv]]
	[[Category: Choi, H K]]		[[Category: Choi, H K]]
	[[Category: Lu, G]]		[[Category: Lu, G]]

OCA at 19:30, 24 December 2014

2014-12-24T19:30:26Z

←Older revision		Revision as of 19:30, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLS_SFV POLS_SFV]] Capsid protein possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E3 protein's function is unknown.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E2 is responsible for viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> 6K is a constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref> E1 is a class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.<ref>PMID:1962454</ref> <ref>PMID:1433520</ref> <ref>PMID:7983743</ref> <ref>PMID:15954801</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Semliki forest virus]]		[[Category: Semliki forest virus]]
-	[[Category: Choi, H K.]]	+	[[Category: Choi, H K]]
-	[[Category: Lu, G.]]	+	[[Category: Lu, G]]
-	[[Category: Rossmann, M G.]]	+	[[Category: Rossmann, M G]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
	[[Category: Nucleocapsid protein]]		[[Category: Nucleocapsid protein]]

OCA at 21:58, 28 September 2014

2014-09-28T21:58:44Z

←Older revision		Revision as of 21:58, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1vcq.~~png\|left~~\|200px]]	+	==SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)==
		+	<StructureSection load='1vcq' size='340' side='right' caption='[[1vcq]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCQ 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=1vcq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vcq RCSB], [http://www.ebi.ac.uk/pdbsum/1vcq 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/vc/1vcq_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 ==
		+	Alphaviruses are enveloped, insect-borne viruses, which contains a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 A and 3.3 A resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize in the same monomer surface regions as found in the crystalline dimer interfaces.

-	~~{{STRUCTURE_1vcq\| PDB=1vcq \| SCENE= }}~~	+	Structure of Semliki Forest virus core protein.,Choi HK, Lu G, Lee S, Wengler G, Rossmann MG Proteins. 1997 Mar;27(3):345-59. PMID:9094737<ref>PMID:9094737</ref>

-	~~===SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9094737}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1vcq]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Semliki_forest_virus Semliki forest virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA].~~	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009094737<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Semliki forest virus]]		[[Category: Semliki forest virus]]
	[[Category: Choi, H K.]]		[[Category: Choi, H K.]]

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

2012-10-20T08:25:29Z

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

←Older revision

Revision as of 08:25, 20 October 2012

OCA at 08:25, 20 October 2012

2012-10-20T08:25:27Z

←Older revision		Revision as of 08:25, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1vcq.png\|left\|200px]]		[[Image:1vcq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1vcq", 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_1vcq\| PDB=1vcq \| SCENE= }}		{{STRUCTURE_1vcq\| PDB=1vcq \| SCENE= }}

	===SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)===		===SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9094737}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9094737 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9094737}}		{{ABSTRACT_PUBMED_9094737}}

	==About this Structure==		==About this Structure==
-	~~1VCQ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA].	+	[[1vcq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Semliki_forest_virus Semliki forest virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCQ OCA].
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9094737~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009094737</ref><references group="xtra"/>
	[[Category: Semliki forest virus]]		[[Category: Semliki forest virus]]
	[[Category: Choi, H K.]]		[[Category: Choi, H K.]]
Line 32:		Line 23:
	[[Category: Polyprotein]]		[[Category: Polyprotein]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
		+	[[Category: Viral protein]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:45:24 2009''