6nk5 - Revision history

OCA at 03:25, 11 April 2020

OCA — Sat, 11 Apr 2020 03:25:27 GMT

←Older revision		Revision as of 03:25, 11 April 2020
Line 3:		Line 3:
	<SX load='6nk5' size='340' side='right' viewer='molstar' caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>		<SX load='6nk5' size='340' side='right' viewer='molstar' caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nk5]] is a 12 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=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nk5]] is a 12 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=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nk5 OCA], [http://pdbe.org/6nk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nk5 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=6nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nk5 OCA], [http://pdbe.org/6nk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nk5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:38, 5 March 2020

OCA — Thu, 05 Mar 2020 04:38:22 GMT

←Older revision		Revision as of 04:38, 5 March 2020
Line 1:		Line 1:

	==Electron Cryo-Microscopy Of Chikungunya VLP==		==Electron Cryo-Microscopy Of Chikungunya VLP==
-	<~~StructureSection~~ load='6nk5' size='340' side='right'caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>	+	<SX load='6nk5' size='340' side='right' viewer='molstar' caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6nk5]] is a 12 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=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6nk5]] is a 12 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=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Chik3]]		[[Category: Chik3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:39, 29 May 2019

OCA — Wed, 29 May 2019 06:39:45 GMT

←Older revision		Revision as of 06:39, 29 May 2019
Line 3:		Line 3:
	<StructureSection load='6nk5' size='340' side='right'caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>		<StructureSection load='6nk5' size='340' side='right'caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nk5]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nk5]] is a 12 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=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nk5 OCA], [http://pdbe.org/6nk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nk5 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nk5 OCA], [http://pdbe.org/6nk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nk5 ProSAT]</span></td></tr>
Line 9:		Line 9:
	== 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 ==
		+	Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 A resolution X-ray crystal structure of Mxra8 and 4 to 5 A resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors.
		+
		+	Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.,Basore K, Kim AS, Nelson CA, Zhang R, Smith BK, Uranga C, Vang L, Cheng M, Gross ML, Smith J, Diamond MS, Fremont DH Cell. 2019 May 6. pii: S0092-8674(19)30392-7. doi: 10.1016/j.cell.2019.04.006. PMID:31080061<ref>PMID:31080061</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nk5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chik3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Basore, K]]		[[Category: Basore, K]]

OCA at 06:52, 23 May 2019

OCA — Thu, 23 May 2019 06:52:53 GMT

←Older revision		Revision as of 06:52, 23 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nk5 is ~~ON HOLD until Paper Publication~~	+	==Electron Cryo-Microscopy Of Chikungunya VLP==
-		+	<StructureSection load='6nk5' size='340' side='right'caption='[[6nk5]], [[Resolution\|resolution]] 4.16Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nk5]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NK5 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nk5 OCA], [http://pdbe.org/6nk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nk5 ProSAT]</span></td></tr>
		+	</table>
		+	== 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).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Basore, K]]
		+	[[Category: Structural genomic]]
		+	[[Category: Fremont, D H]]
		+	[[Category: Chikungunya]]
		+	[[Category: Csgid]]
		+	[[Category: Virus like particle]]
		+	[[Category: Virus-like particle]]

OCA at 13:41, 27 February 2019

OCA — Wed, 27 Feb 2019 13:41:53 GMT

←Older revision		Revision as of 13:41, 27 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nk5 is ON HOLD	+	The entry 6nk5 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 07:33, 13 February 2019

OCA — Wed, 13 Feb 2019 07:33:51 GMT

←Older revision		Revision as of 07:33, 13 February 2019
Line 3:		Line 3:
	The entry 6nk5 is ON HOLD		The entry 6nk5 is ON HOLD

-	Authors: ~~Nelson, C.A., Fremont, D.H.~~	+	Authors:

-	Description: ~~Electron Cryo-Microscopy Of Chikungunya VLP~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Fremont, D.H]]
-	[[Category: Nelson, C.A]]

OCA: Protected "6nk5" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2019 10:40:54 GMT

Protected "6nk5" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:40, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nk5 is ON HOLD Authors: Nelson, C.A., Fremont, D.H. Description: Electron Cryo-Microscopy Of Chikungunya VLP Category: Unreleased Structures [...

OCA — Wed, 16 Jan 2019 10:40:53 GMT

New page: '''Unreleased structure''' The entry 6nk5 is ON HOLD Authors: Nelson, C.A., Fremont, D.H. Description: Electron Cryo-Microscopy Of Chikungunya VLP Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 6nk5 is ON HOLD

Authors: Nelson, C.A., Fremont, D.H.

Description: Electron Cryo-Microscopy Of Chikungunya VLP
[[Category: Unreleased Structures]]
[[Category: Fremont, D.H]]
[[Category: Nelson, C.A]]