5h23 - Revision history

OCA at 07:21, 9 August 2023

OCA — Wed, 09 Aug 2023 07:21:25 GMT

←Older revision		Revision as of 07:21, 9 August 2023
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	<StructureSection load='5h23' size='340' side='right'caption='[[5h23]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5h23' size='340' side='right'caption='[[5h23]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h23]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chikv Chikv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H23 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h23]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H23 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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]] 2.2Å</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=5h23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h23 OCA], [~~http~~://pdbe.org/5h23 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h23 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h23 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h23 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=5h23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h23 OCA], [https://pdbe.org/5h23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h23 RCSB], [https://www.ebi.ac.uk/pdbsum/5h23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h23 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POLSF_CHIKS POLSF_CHIKS] Forms an icosahedral capsid with a T=4 symmetry composed of 240 copies of the capsid protein surrounded by a lipid membrane through which penetrate 80 spikes composed of trimers of E1-E2 heterodimers (By similarity). The capsid protein binds to the viral RNA genome at a site adjacent to a ribosome binding site for viral genome translation following genome release (By similarity). Possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein (By similarity). 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 icosahedric core particles (By similarity). The resulting nucleocapsid eventually associates with the cytoplasmic domain of the spike glycoprotein E2 at the cell membrane, leading to budding and formation of mature virions (By similarity). In case of infection, new virions attach to target cells and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane (By similarity). This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible (By similarity). The uncoating might be triggered by the interaction of capsid proteins with ribosomes (By similarity). Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding (By similarity). Specifically inhibits interleukin-1 receptor-associated kinase 1/IRAK1-dependent signaling during viral entry, representing a means by which the alphaviruses may evade innate immune detection and activation prior to viral gene expression (By similarity).[UniProtKB:P03315][UniProtKB:P03316][UniProtKB:P27284] Provides the signal sequence for the translocation of the precursor of protein E3/E2 to the host endoplasmic reticulum. Furin-cleaved E3 remains associated with spike glycoprotein E1 and mediates pH protection of the latter during the transport via the secretory pathway. After virion release from the host cell, the assembly protein E3 is gradually released in the extracellular space.[UniProtKB:P03315] Plays a role in 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.[UniProtKB:P03315] Plays a role in viral assembly and release.[UniProtKB:P0DOK0]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5h23" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5h23" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Chikv]]
-	[[Category: Large Structures]]
-	[[Category: Kesari, P]]
-	[[Category: Kumar, P]]
-	[[Category: Sharma, R]]
-	[[Category: Tomar, S]]
-	[[Category: Capsid protein]]
	[[Category: Chikungunya virus]]		[[Category: Chikungunya virus]]
-	[[Category: ~~Viral protein~~]]	+	[[Category: Large Structures]]
		+	[[Category: Kesari P]]
		+	[[Category: Kumar P]]
		+	[[Category: Sharma R]]
		+	[[Category: Tomar S]]

OCA at 07:56, 3 April 2019

OCA — Wed, 03 Apr 2019 07:56:15 GMT

←Older revision		Revision as of 07:56, 3 April 2019
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	==Crystal structure of Chikungunya virus capsid protein==		==Crystal structure of Chikungunya virus capsid protein==
-	<StructureSection load='5h23' size='340' side='right' caption='[[5h23]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5h23' size='340' side='right'caption='[[5h23]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h23]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h23]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chikv Chikv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H23 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5h23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h23 OCA], [http://pdbe.org/5h23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h23 RCSB], [http://www.ebi.ac.uk/pdbsum/5h23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h23 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=5h23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h23 OCA], [http://pdbe.org/5h23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h23 RCSB], [http://www.ebi.ac.uk/pdbsum/5h23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h23 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of chikungunya (CHIKV) virus capsid protease domain has been determined at 2.2A. Structure reveals a chymotrypsin-like protease fold with a conserved hydrophobic pocket in CHIKV capsid protein (CP) for interaction with the cytoplasmic tail of E2 (cdE2) similar to the capsid protein of other alphaviruses. Molecular contacts between CP-cdE2 were determined by fitting structures of CHIKV CP and cdE2 into the cryo-EM map of Venezuelan equine encephalitis virus (VEEV). Binding of (S)-(+)-Mandelic acid (MDA) and Ethyl 3-aminobenzoate (EAB) to the hydrophobic pocket of CP was evaluated by molecular docking. Surface plasmon resonance (SPR) and fluorescence spectroscopy experiments confirmed MDA and EAB binding to the CP. The binding constants (KD) obtained from SPR for MDA and EAB were 1.2 x 10(-3) M and 0.2 x 10(-9) M, respectively. This study adds to the understanding of chikungunya virus structural proteins and may serve as the basis for antiviral development against chikungunya disease.
		+
		+	Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket.,Sharma R, Kesari P, Kumar P, Tomar S Virology. 2018 Feb;515:223-234. doi: 10.1016/j.virol.2017.12.020. Epub 2018 Jan, 5. PMID:29306785<ref>PMID:29306785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5h23" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chikv]]
		+	[[Category: Large Structures]]
	[[Category: Kesari, P]]		[[Category: Kesari, P]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]

OCA at 06:16, 14 March 2018

OCA — Wed, 14 Mar 2018 06:16:43 GMT

←Older revision		Revision as of 06:16, 14 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5h23 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Chikungunya virus capsid protein==
-		+	<StructureSection load='5h23' size='340' side='right' caption='[[5h23]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Sharma, R~~., ~~Kesari~~, P., ~~Tomar~~, S., ~~Kumar~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5h23]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H23 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H23 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Chikungunya virus capsid protein~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5h23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h23 OCA], [http://pdbe.org/5h23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h23 RCSB], [http://www.ebi.ac.uk/pdbsum/5h23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h23 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kesari, P]]		[[Category: Kesari, P]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
		+	[[Category: Sharma, R]]
	[[Category: Tomar, S]]		[[Category: Tomar, S]]
-	[[Category: ~~Sharma, R~~]]	+	[[Category: Capsid protein]]
		+	[[Category: Chikungunya virus]]
		+	[[Category: Viral protein]]

OCA at 03:32, 8 March 2018

OCA — Thu, 08 Mar 2018 03:32:57 GMT

←Older revision		Revision as of 03:32, 8 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h23 is ON HOLD	+	The entry 5h23 is ON HOLD until Paper Publication

	Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.		Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.

OCA at 04:45, 28 February 2018

OCA — Wed, 28 Feb 2018 04:45:10 GMT

←Older revision		Revision as of 04:45, 28 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h23 is ON HOLD ~~until Paper Publication~~	+	The entry 5h23 is ON HOLD

	Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.		Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.

OCA at 10:41, 27 September 2017

OCA — Wed, 27 Sep 2017 10:41:26 GMT

←Older revision		Revision as of 10:41, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h23 is ON HOLD until ~~Oct 14 2018~~	+	The entry 5h23 is ON HOLD until Paper Publication

	Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.		Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.
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	Description: Crystal structure of Chikungunya virus capsid protein		Description: Crystal structure of Chikungunya virus capsid protein
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kumar, P]]
	[[Category: Kesari, P]]		[[Category: Kesari, P]]
		+	[[Category: Kumar, P]]
	[[Category: Tomar, S]]		[[Category: Tomar, S]]
	[[Category: Sharma, R]]		[[Category: Sharma, R]]

OCA at 13:14, 26 October 2016

OCA — Wed, 26 Oct 2016 13:14:27 GMT

←Older revision		Revision as of 13:14, 26 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h23 is ON HOLD	+	The entry 5h23 is ON HOLD until Oct 14 2018

	Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.		Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.

-	Description: Crystal structure of Chikungunya virus capsid protein ~~(106-261)~~	+	Description: Crystal structure of Chikungunya virus capsid protein
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]

OCA: Protected "5h23" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2016 12:03:55 GMT

Protected "5h23" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5h23 is ON HOLD Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P. Description: Crystal structure of Chikungunya virus capsid protein (106-261) ...

OCA — Wed, 19 Oct 2016 12:03:53 GMT

New page: '''Unreleased structure''' The entry 5h23 is ON HOLD Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P. Description: Crystal structure of Chikungunya virus capsid protein (106-261) ...

New page

'''Unreleased structure'''

The entry 5h23 is ON HOLD

Authors: Sharma, R., Kesari, P., Tomar, S., Kumar, P.

Description: Crystal structure of Chikungunya virus capsid protein (106-261)
[[Category: Unreleased Structures]]
[[Category: Kumar, P]]
[[Category: Kesari, P]]
[[Category: Tomar, S]]
[[Category: Sharma, R]]