5vu2 - Revision history

OCA at 22:13, 10 April 2020

OCA — Fri, 10 Apr 2020 22:13:17 GMT

←Older revision		Revision as of 22:13, 10 April 2020
Line 3:		Line 3:
	<SX load='5vu2' size='340' side='right' viewer='molstar' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>		<SX load='5vu2' size='340' side='right' viewer='molstar' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHIKVgp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371095 CHIK3])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHIKVgp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371095 CHIK3])</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=5vu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu2 OCA], [http://pdbe.org/5vu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu2 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=5vu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu2 OCA], [http://pdbe.org/5vu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:34, 5 March 2020

OCA — Thu, 05 Mar 2020 04:34:25 GMT

←Older revision		Revision as of 04:34, 5 March 2020
Line 1:		Line 1:

	==Electron cryo-microscopy of "immature" Chikungunya VLP==		==Electron cryo-microscopy of "immature" Chikungunya VLP==
-	<~~StructureSection~~ load='5vu2' size='340' side='right'caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>	+	<SX load='5vu2' size='340' side='right' viewer='molstar' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Chik3]]		[[Category: Chik3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 17:24, 11 December 2019

OCA — Wed, 11 Dec 2019 17:24:47 GMT

←Older revision		Revision as of 17:24, 11 December 2019
Line 1:		Line 1:

	==Electron cryo-microscopy of "immature" Chikungunya VLP==		==Electron cryo-microscopy of "immature" Chikungunya VLP==
-	<StructureSection load='5vu2' size='340' side='right' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>	+	<StructureSection load='5vu2' size='340' side='right'caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Chik3]]		[[Category: Chik3]]
		+	[[Category: Large Structures]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]
	[[Category: Yap, M L]]		[[Category: Yap, M L]]

OCA at 06:43, 20 December 2017

OCA — Wed, 20 Dec 2017 06:43:18 GMT

←Older revision		Revision as of 06:43, 20 December 2017
Line 3:		Line 3:
	<StructureSection load='5vu2' size='340' side='right' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>		<StructureSection load='5vu2' size='340' side='right' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Chik3 Chik3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 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=5vu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu2 OCA], [http://pdbe.org/5vu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu2 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHIKVgp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=371095 CHIK3])</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=5vu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu2 OCA], [http://pdbe.org/5vu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/POLS_CHIK3 POLS_CHIK3]] 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 endocytosis their membrane fuses with the target cell 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 (By similarity). E3 protein's function is unknown (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity).		[[http://www.uniprot.org/uniprot/POLS_CHIK3 POLS_CHIK3]] 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 endocytosis their membrane fuses with the target cell 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 (By similarity). E3 protein's function is unknown (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-A resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
		+
		+	Structural studies of Chikungunya virus maturation.,Yap ML, Klose T, Urakami A, Hasan SS, Akahata W, Rossmann MG Proc Natl Acad Sci U S A. 2017 Dec 4. pii: 1713166114. doi:, 10.1073/pnas.1713166114. PMID:29203665<ref>PMID:29203665</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vu2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chik3]]
	[[Category: Rossmann, M G]]		[[Category: Rossmann, M G]]
	[[Category: Yap, M L]]		[[Category: Yap, M L]]

OCA at 07:16, 6 December 2017

OCA — Wed, 06 Dec 2017 07:16:48 GMT

←Older revision		Revision as of 07:16, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vu2 ~~is ON HOLD until Paper Publication~~	+	==Electron cryo-microscopy of "immature" Chikungunya VLP==
-		+	<StructureSection load='5vu2' size='340' side='right' caption='[[5vu2]], [[Resolution\|resolution]] 6.80Å' scene=''>
-	~~Authors~~: ~~Rossmann~~, M.G., ~~Yap~~, M.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vu2]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU2 FirstGlance]. <br>
-	~~Description~~: ~~Electron cryo~~-~~microscopy~~ of ~~""immature"" Chikungunya VLP~~	+	</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=5vu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu2 OCA], [http://pdbe.org/5vu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu2 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Yap, M.L]]	+	== Function ==
-	[[Category: ~~Rossmann, M.G~~]]	+	[[http://www.uniprot.org/uniprot/POLS_CHIK3 POLS_CHIK3]] 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 endocytosis their membrane fuses with the target cell 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 (By similarity). E3 protein's function is unknown (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Rossmann, M G]]
		+	[[Category: Yap, M L]]
		+	[[Category: Chikungunya]]
		+	[[Category: Immature]]
		+	[[Category: Virus]]
		+	[[Category: Virus like particle]]

OCA at 14:13, 27 September 2017

OCA — Wed, 27 Sep 2017 14:13:32 GMT

←Older revision		Revision as of 14:13, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vu2 is ON HOLD	+	The entry 5vu2 is ON HOLD until Paper Publication

-	Authors: ~~Michael G~~ Rossmann, ~~Moh Lan~~ Yap	+	Authors: Rossmann, M.G., Yap, M.L.

-	Description: Electron ~~Cryo~~-microscopy of "immature" Chikungunya VLP	+	Description: Electron cryo-microscopy of ""immature"" Chikungunya VLP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Michael G~~ Rossmann, ~~Moh Lan Yap~~]]	+	[[Category: Yap, M.L]]
		+	[[Category: Rossmann, M.G]]

OCA: Protected "5vu2" [edit=sysop:move=sysop]

OCA — Wed, 24 May 2017 11:50:35 GMT

Protected "5vu2" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:50, 24 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vu2 is ON HOLD Authors: Michael G Rossmann, Moh Lan Yap Description: Electron Cryo-microscopy of "immature" Chikungunya VLP [[Category: Unreleased...

OCA — Wed, 24 May 2017 11:50:34 GMT

New page: '''Unreleased structure''' The entry 5vu2 is ON HOLD Authors: Michael G Rossmann, Moh Lan Yap Description: Electron Cryo-microscopy of "immature" Chikungunya VLP [[Category: Unreleased...

New page

'''Unreleased structure'''

The entry 5vu2 is ON HOLD

Authors: Michael G Rossmann, Moh Lan Yap

Description: Electron Cryo-microscopy of "immature" Chikungunya VLP
[[Category: Unreleased Structures]]
[[Category: Michael G Rossmann, Moh Lan Yap]]