7buf - Revision history

OCA at 05:55, 3 July 2025

2025-07-03T05:55:53Z

← Older revision		Revision as of 05:55, 3 July 2025
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	==Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG==		==Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG==
	<~~StructureSection~~ load='7buf' size='340' side='right'caption='[[7buf]], [[Resolution\|resolution]] 6.10Å' scene=''>		<SX load='7buf' size='340' side='right' viewer='molstar' caption='[[7buf]], [[Resolution\|resolution]] 6.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7buf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BUF FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BUF FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 6.1Å</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 6.1Å</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=7buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7buf OCA], [https://pdbe.org/7buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7buf RCSB], [https://www.ebi.ac.uk/pdbsum/7buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7buf 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=7buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7buf OCA], [https://pdbe.org/7buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7buf RCSB], [https://www.ebi.ac.uk/pdbsum/7buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7buf ProSAT]</span></td></tr>
	</table>		</table>
	== ~~Function~~ ==		<div style="background-color:#fffaf0;">
	~~[https~~:~~//www~~.~~uniprot~~.~~org/uniprot/E0WXJ2_9FLAV E0WXJ2_9FLAV] Component~~ of the ~~viral RNA replication~~ complex ~~that functions~~ in ~~virion assembly and antagonizes~~ the ~~host immune response~~.~~[ARBA~~:~~ARBA00024317] Functions as~~ a ~~signal peptide for NS4B and is required for the interferon antagonism activity~~ of the ~~latter~~.~~[ARBA:ARBA00003504] Serine protease subunit NS2B: Required cofactor for the serine protease function~~ of ~~NS3~~.~~[PROSITE~~-~~ProRule~~:~~PRU00859]~~		== Publication Abstract from PubMed ==
			Human antibody SIgN-3C neutralizes dengue virus (DENV) and Zika virus (ZIKV) differently. DENV:SIgN-3C Fab and ZIKV:SIgN-3C Fab cryoelectron microscopy (cryo-EM) complex structures show Fabs crosslink E protein dimers at extracellular pH 8.0 condition and also when further incubated at acidic endosomal conditions (pH 8.0-6.5). We observe Fab binding to DENV (pH 8.0-5.0) prevents virus fusion, and the number of bound Fabs increase (from 120 to 180). For ZIKV, although there are already 180 copies of Fab at pH 8.0, virus structural changes at pH 5.0 are not inhibited. The immunoglobulin G (IgG):DENV structure at pH 8.0 shows both Fab arms bind to epitopes around the 2-fold vertex. On ZIKV, an additional Fab around the 5-fold vertex at pH 8.0 suggests one IgG arm would engage with an epitope, although the other may bind to other viruses, causing aggregation. For DENV2 at pH 5.0, a similar scenario would occur, suggesting DENV2:IgG complex would aggregate in the endosome. Hence, a single antibody employs different neutralization mechanisms against different flaviviruses.

			A Human Antibody Neutralizes Different Flaviviruses by Using Different Mechanisms.,Zhang S, Loy T, Ng TS, Lim XN, Chew SV, Tan TY, Xu M, Kostyuchenko VA, Tukijan F, Shi J, Fink K, Lok SM Cell Rep. 2020 Apr 28;31(4):107584. doi: 10.1016/j.celrep.2020.107584. PMID:32348755<ref>PMID:32348755</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7buf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	~~[[Category: Dengue virus 2]]~~
	~~[[Category: Homo sapiens]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chew SV]]		[[Category: Chew SV]]

OCA at 10:49, 27 March 2024

2024-03-27T10:49:28Z

← Older revision		Revision as of 10:49, 27 March 2024
Line 1:		Line 1:

	==Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG==		==Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG==
	<StructureSection load='7buf' size='340' side='right'caption='[[7buf]]' scene=''>		<StructureSection load='7buf' size='340' side='right'caption='[[7buf]], [[Resolution\|resolution]] 6.10Å' 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=7BUF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BUF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7buf]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BUF FirstGlance]. <br>
	</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=7buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7buf OCA], [~~http~~://pdbe.org/7buf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7buf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7buf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7buf ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 6.1Å</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=7buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7buf OCA], [https://pdbe.org/7buf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7buf RCSB], [https://www.ebi.ac.uk/pdbsum/7buf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7buf ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/E0WXJ2_9FLAV E0WXJ2_9FLAV] Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response.[ARBA:ARBA00024317] Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.[ARBA:ARBA00003504] Serine protease subunit NS2B: Required cofactor for the serine protease function of NS3.[PROSITE-ProRule:PRU00859]

			==See Also==
			*[[Antibody 3D structures\|Antibody 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Dengue virus 2]]
			[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chew SV]]		[[Category: Chew SV]]

OCA at 05:39, 13 May 2020

2020-05-13T05:39:24Z

← Older revision		Revision as of 05:39, 13 May 2020
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7buf ~~is ON HOLD until Paper Publication~~		==Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG==
			<StructureSection load='7buf' size='340' side='right'caption='[[7buf]]' scene=''>
	~~Authors~~: ~~Zhang, S~~.~~, Chew, S~~.V., ~~Lim, X~~.N., Ng, T.S., ~~Kostyuchenko, V~~.A., ~~Lok, S~~.M.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BUF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BUF FirstGlance]. <br>
	~~Description: Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG~~		</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=7buf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7buf OCA], [http://pdbe.org/7buf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7buf RCSB], [http://www.ebi.ac.uk/pdbsum/7buf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7buf ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Zhang, S~~]]		__TOC__
	[[Category: ~~Lok, S.M~~]]		</StructureSection>
	[[Category: ~~Ng, T.S~~]]		[[Category: Large Structures]]
	[[Category: ~~Chew, S.V~~]]		[[Category: Chew SV]]
	[[Category: ~~Lim, X.N~~]]		[[Category: Kostyuchenko VA]]
	[[Category: ~~Kostyuchenko, V.A~~]]		[[Category: Lim XN]]
			[[Category: Lok SM]]
			[[Category: Ng TS]]
			[[Category: Zhang S]]

OCA at 05:34, 29 April 2020

2020-04-29T05:34:14Z

← Older revision		Revision as of 05:34, 29 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Zhang, S., Chew, S.V., Lim, X.N., Ng, T.S., Kostyuchenko, V.A., Lok, S.M.		Authors: Zhang, S., Chew, S.V., Lim, X.N., Ng, T.S., Kostyuchenko, V.A., Lok, S.M.
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	Description: Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG		Description: Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Zhang, S]]
	[[Category: Lok, S.M]]		[[Category: Lok, S.M]]
	~~[[Category: Kostyuchenko, V.A]]~~
	~~[[Category: Zhang, S]]~~
	[[Category: Ng, T.S]]		[[Category: Ng, T.S]]
	[[Category: Chew, S.V]]		[[Category: Chew, S.V]]
	[[Category: Lim, X.N]]		[[Category: Lim, X.N]]
			[[Category: Kostyuchenko, V.A]]

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

2020-04-15T05:42:12Z

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

← Older revision	Revision as of 05:42, 15 April 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7buf is ON HOLD Authors: Zhang, S., Chew, S.V., Lim, X.N., Ng, T.S., Kostyuchenko, V.A., Lok, S.M. Description: Cryo-EM structure of Dengue virus s...

2020-04-15T05:42:11Z

New page: '''Unreleased structure''' The entry 7buf is ON HOLD Authors: Zhang, S., Chew, S.V., Lim, X.N., Ng, T.S., Kostyuchenko, V.A., Lok, S.M. Description: Cryo-EM structure of Dengue virus s...

New page

'''Unreleased structure'''

The entry 7buf is ON HOLD

Authors: Zhang, S., Chew, S.V., Lim, X.N., Ng, T.S., Kostyuchenko, V.A., Lok, S.M.

Description: Cryo-EM structure of Dengue virus serotype 2 complexed with SIgN-3C IgG
[[Category: Unreleased Structures]]
[[Category: Lok, S.M]]
[[Category: Kostyuchenko, V.A]]
[[Category: Zhang, S]]
[[Category: Ng, T.S]]
[[Category: Chew, S.V]]
[[Category: Lim, X.N]]