OCA at 15:58, 18 October 2023

2023-10-18T15:58:23Z

←Older revision		Revision as of 15:58, 18 October 2023
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-	====	+	==Crystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Far Eastern Subtype)==
-	<StructureSection load='7lse' size='340' side='right'caption='[[7lse]]' scene=''>	+	<StructureSection load='7lse' size='340' side='right'caption='[[7lse]], [[Resolution\|resolution]] 2.35Å' 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'>[[7lse]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Tick-borne_encephalitis_virus_(STRAIN_SOFJIN) Tick-borne encephalitis virus (STRAIN SOFJIN)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LSE 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=7lse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lse OCA], [https://pdbe.org/7lse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lse RCSB], [https://www.ebi.ac.uk/pdbsum/7lse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lse 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]] 2.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7lse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lse OCA], [https://pdbe.org/7lse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lse RCSB], [https://www.ebi.ac.uk/pdbsum/7lse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lse ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POLG_TBEVS POLG_TBEVS] Plays a role in virus budding by binding to the cell membrane and gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. During virus entry, may induce genome penetration into the host cytoplasm after hemifusion induced by the surface proteins. Can migrate to the cell nucleus where it modulates host functions.[UniProtKB:P17763] Inhibits RNA silencing by interfering with host Dicer.[UniProtKB:P03314] Prevents premature fusion activity of envelope proteins in trans-Golgi by binding to envelope protein E at pH6.0. After virion release in extracellular space, gets dissociated from E dimers.[UniProtKB:P17763] Acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is the only viral peptide matured by host furin in the trans-Golgi network probably to avoid catastrophic activation of the viral fusion activity in acidic Golgi compartment prior to virion release. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.[UniProtKB:P17763] May play a role in virus budding. Exerts cytotoxic effects by activating a mitochondrial apoptotic pathway through M ectodomain. May display a viroporin activity.[UniProtKB:P17763] Binds to host cell surface receptor and mediates fusion between viral and cellular membranes. Envelope protein is synthesized in the endoplasmic reticulum in the form of heterodimer with protein prM. They play a role in virion budding in the ER, and the newly formed immature particle is covered with 60 spikes composed of heterodimer between precursor prM and envelope protein E. The virion is transported to the Golgi apparatus where the low pH causes dissociation of PrM-E heterodimers and formation of E homodimers. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM would play a role in immune evasion.[UniProtKB:P17763] Involved in immune evasion, pathogenesis and viral replication. Once cleaved off the polyprotein, is targeted to three destinations: the viral replication cycle, the plasma membrane and the extracellular compartment. Essential for viral replication. Required for formation of the replication complex and recruitment of other non-structural proteins to the ER-derived membrane structures. Excreted as a hexameric lipoparticle that plays a role against host immune response. Antagonizing the complement function. Binds to the host macrophages and dendritic cells. Inhibits signal transduction originating from Toll-like receptor 3 (TLR3).[UniProtKB:Q9Q6P4] Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response.[UniProtKB:P17763] Required cofactor for the serine protease function of NS3 (By similarity). May have membrane-destabilizing activity and form viroporins (By similarity).[UniProtKB:P17763][PROSITE-ProRule:PRU00859] 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.[PROSITE-ProRule:PRU00860] Regulates the ATPase activity of the NS3 helicase activity. NS4A allows NS3 helicase to conserve energy during unwinding.[UniProtKB:Q9Q6P4] Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.[UniProtKB:P17763] Induces the formation of ER-derived membrane vesicles where the viral replication takes place. Inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway. Inhibits STAT2 translocation in the nucleus after IFN-alpha treatment.[UniProtKB:Q9Q6P4] 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 RNA genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host TYK2 and STAT2 phosphorylation, thereby preventing activation of JAK-STAT signaling pathway.[UniProtKB:P17763]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI-EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.
		+
		+	Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease.,Agudelo M, Palus M, Keeffe JR, Bianchini F, Svoboda P, Salat J, Peace A, Gazumyan A, Cipolla M, Kapoor T, Guidetti F, Yao KH, Elsterova J, Teislerova D, Chrdle A, Honig V, Oliveira T, West AP, Lee YE, Rice CM, MacDonald MR, Bjorkman PJ, Ruzek D, Robbiani DF, Nussenzweig MC J Exp Med. 2021 May 3;218(5):e20210236. doi: 10.1084/jem.20210236. PMID:33831141<ref>PMID:33831141</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7lse" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Bjorkman PJ]]
		+	[[Category: Keeffe JR]]

OCA at 06:53, 7 April 2021

2021-04-07T06:53:42Z

←Older revision		Revision as of 06:53, 7 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7lse ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7lse' size='340' side='right'caption='[[7lse]]' scene=''>
-	~~Authors~~: ~~Keeffe, J~~.R.~~, Bjorkman, P~~.J.	+	== 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: Crystal structure of~~ the ~~human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Far Eastern Subtype)~~	+	</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=7lse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lse OCA], [https://pdbe.org/7lse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lse RCSB], [https://www.ebi.ac.uk/pdbsum/7lse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lse ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Keeffe~~, J.R]]	+	__TOC__
-	[[Category: ~~Bjorkman, P.J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:23, 17 March 2021

2021-03-17T05:23:27Z

←Older revision		Revision as of 05:23, 17 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7lse is ON HOLD	+	The entry 7lse is ON HOLD until Paper Publication

	Authors: Keeffe, J.R., Bjorkman, P.J.		Authors: Keeffe, J.R., Bjorkman, P.J.

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

2021-02-24T05:43:32Z

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

←Older revision

Revision as of 05:43, 24 February 2021

OCA: New page: '''Unreleased structure''' The entry 7lse is ON HOLD Authors: Keeffe, J.R., Bjorkman, P.J. Description: Crystal structure of the human neutralizing antibody Fab fragment T025 bound to ...

2021-02-24T05:43:31Z

New page: '''Unreleased structure''' The entry 7lse is ON HOLD Authors: Keeffe, J.R., Bjorkman, P.J. Description: Crystal structure of the human neutralizing antibody Fab fragment T025 bound to ...

New page

'''Unreleased structure'''

The entry 7lse is ON HOLD

Authors: Keeffe, J.R., Bjorkman, P.J.

Description: Crystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Far Eastern Subtype)
[[Category: Unreleased Structures]]
[[Category: Keeffe, J.R]]
[[Category: Bjorkman, P.J]]

7lse - Revision history

OCA at 15:58, 18 October 2023

OCA at 06:53, 7 April 2021

OCA at 05:23, 17 March 2021

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

OCA: New page: '''Unreleased structure''' The entry 7lse is ON HOLD Authors: Keeffe, J.R., Bjorkman, P.J. Description: Crystal structure of the human neutralizing antibody Fab fragment T025 bound to ...