7qrf - Revision history

OCA at 13:21, 1 February 2024

2024-02-01T13:21:49Z

← Older revision		Revision as of 13:21, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7qrf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus_(WESTERN_SUBTYPE) Tick-borne encephalitis virus (WESTERN SUBTYPE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QRF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qrf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus_(WESTERN_SUBTYPE) Tick-borne encephalitis virus (WESTERN SUBTYPE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QRF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.28Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qrf OCA], [https://pdbe.org/7qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qrf RCSB], [https://www.ebi.ac.uk/pdbsum/7qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qrf ProSAT]</span></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=7qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qrf OCA], [https://pdbe.org/7qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qrf RCSB], [https://www.ebi.ac.uk/pdbsum/7qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qrf ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:30, 7 December 2022

2022-12-07T08:30:31Z

← Older revision		Revision as of 08:30, 7 December 2022
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	====		==Structure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (E) from tick-borne encephalitis virus==
	<StructureSection load='7qrf' size='340' side='right'caption='[[7qrf]]' scene=''>		<StructureSection load='7qrf' size='340' side='right'caption='[[7qrf]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[7qrf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus_(WESTERN_SUBTYPE) Tick-borne encephalitis virus (WESTERN SUBTYPE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QRF 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=7qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qrf OCA], [https://pdbe.org/7qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qrf RCSB], [https://www.ebi.ac.uk/pdbsum/7qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qrf ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qrf OCA], [https://pdbe.org/7qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qrf RCSB], [https://www.ebi.ac.uk/pdbsum/7qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qrf ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/POLG_TBEVW POLG_TBEVW] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity). prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity). Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity). Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity). Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential). Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity). Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity). Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity). Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity). RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host SCRIB and prevents activation of downstream JAK-STAT signaling pathway (By similarity).
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The flavivirus envelope glycoproteins prM and E drive the assembly of icosahedral, spiky immature particles that bud across the membrane of the endoplasmic reticulum. Maturation into infectious virions in the trans-Golgi network involves an acid-pH-driven rearrangement into smooth particles made of (prM/E)(2) dimers exposing a furin site for prM cleavage into "pr" and "M". Here we show that the prM "pr" moiety derives from an HSP40 cellular chaperonin. Furthermore, the X-ray structure of the tick-borne encephalitis virus (pr/E)(2) dimer at acidic pH reveals the E 150-loop as a hinged-lid that opens at low pH to expose a positively-charged pr-binding pocket at the E dimer interface, inducing (prM/E)(2) dimer formation to generate smooth particles in the Golgi. Furin cleavage is followed by lid-closure upon deprotonation in the neutral-pH extracellular environment, expelling pr while the 150-loop takes the relay in fusion loop protection, thus revealing the elusive flavivirus mechanism of fusion activation.

			Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery.,Vaney MC, Dellarole M, Duquerroy S, Medits I, Tsouchnikas G, Rouvinski A, England P, Stiasny K, Heinz FX, Rey FA Nat Commun. 2022 Jun 28;13(1):3718. doi: 10.1038/s41467-022-31111-y. PMID:35764616<ref>PMID:35764616</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7qrf" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Rey FA]]
			[[Category: Rouvinski A]]
			[[Category: Vaney MC]]

OCA at 07:58, 25 May 2022

2022-05-25T07:58:11Z

← Older revision		Revision as of 07:58, 25 May 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7qrf is ~~ON HOLD until Paper Publication~~		====
			<StructureSection load='7qrf' size='340' side='right'caption='[[7qrf]]' scene=''>
	~~Authors:~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description~~:		</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=7qrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qrf OCA], [https://pdbe.org/7qrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qrf RCSB], [https://www.ebi.ac.uk/pdbsum/7qrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qrf ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Z-disk]]

OCA at 04:46, 9 March 2022

2022-03-09T04:46:44Z

← Older revision		Revision as of 04:46, 9 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7qrf is ON HOLD		The entry 7qrf is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7qrf" [edit=sysop:move=sysop]

2022-01-19T05:50:57Z

Protected "7qrf" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:50, 19 January 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7qrf is ON HOLD Authors: Description: Category: Unreleased Structures

2022-01-19T05:50:56Z

New page: '''Unreleased structure''' The entry 7qrf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7qrf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]