5gjt - Revision history

OCA at 11:33, 2 August 2023

OCA — Wed, 02 Aug 2023 11:33:41 GMT

←Older revision		Revision as of 11:33, 2 August 2023
Line 1:		Line 1:

	==Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1==		==Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1==
-	<StructureSection load='5gjt' size='340' side='right' caption='[[5gjt]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='5gjt' size='340' side='right'caption='[[5gjt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gjt]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Influenza_a_virus_~~(a/~~washington~~/05/2011(~~h1n1~~)) Influenza a virus (a/~~washington~~/05/2011(~~h1n1~~))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gjt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Washington/05/2011(H1N1)) Influenza A virus (A/Washington/05/2011(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJT 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.1Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5gjs\|5gjs~~]]</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1318439 Influenza A virus (A~~/~~Washington/05/2011(H1N1))])~~</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=5gjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjt OCA], [https://pdbe.org/5gjt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gjt RCSB], [https://www.ebi.ac.uk/pdbsum/5gjt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjt 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=5gjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjt OCA], [~~http~~://pdbe.org/5gjt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gjt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gjt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjt ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/N0C8E5_9INFA N0C8E5_9INFA]] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.[RuleBase:RU003324][SAAS:SAAS00363335]	+	[https://www.uniprot.org/uniprot/N0C8E5_9INFA N0C8E5_9INFA] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.[RuleBase:RU003324][SAAS:SAAS00363335]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[Hemagglutinin\|Hemagglutinin]]	+	*[[Hemagglutinin 3D structures\|Hemagglutinin 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Ding, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Wang, W~~]]	+	[[Category: Ding J]]
-	[[Category: ~~Zhang, T~~]]	+	[[Category: Wang W]]
-	[[Category: ~~Complementarity determining region]]~~	+	[[Category: Zhang T]]
-	~~[[Category: Epitope]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Paratope~~]]	+

OCA at 08:00, 14 June 2018

OCA — Thu, 14 Jun 2018 08:00:27 GMT

←Older revision		Revision as of 08:00, 14 June 2018
Line 3:		Line 3:
	<StructureSection load='5gjt' size='340' side='right' caption='[[5gjt]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='5gjt' size='340' side='right' caption='[[5gjt]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gjt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GJT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gjt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/washington/05/2011(h1n1)) Influenza a virus (a/washington/05/2011(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GJT 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gjs\|5gjs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gjs\|5gjs]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1318439 Influenza A virus (A/Washington/05/2011(H1N1))])</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=5gjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjt OCA], [http://pdbe.org/5gjt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjt RCSB], [http://www.ebi.ac.uk/pdbsum/5gjt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjt 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=5gjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjt OCA], [http://pdbe.org/5gjt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjt RCSB], [http://www.ebi.ac.uk/pdbsum/5gjt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjt ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5gjt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gjt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Hemagglutinin\|Hemagglutinin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Ding, J]]		[[Category: Ding, J]]
	[[Category: Wang, W]]		[[Category: Wang, W]]

OCA at 14:39, 22 December 2016

OCA — Thu, 22 Dec 2016 14:39:35 GMT

←Older revision		Revision as of 14:39, 22 December 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/N0C8E5_9INFA N0C8E5_9INFA]] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.[RuleBase:RU003324][SAAS:SAAS00363335]		[[http://www.uniprot.org/uniprot/N0C8E5_9INFA N0C8E5_9INFA]] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.[RuleBase:RU003324][SAAS:SAAS00363335]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	As influenza A viruses remain a major threat to human health worldwide, the discovery of broadly neutralizing monoclonal antibodies that recognize conserved epitopes would facilitate the development of antibody-based therapeutic strategies. Here we report that a VH4-4-encoded human mAb named 3E1 could neutralize H1 and H5 subtype viruses in vitro and protect mice against the H1N1 and H5N6 viruses by inhibiting the low pH-induced conformational rearrangement of haemagglutinin (HA), hence blocking membrane fusion. The crystal structures of 3E1 Fab in complex with HA of two H1N1 strains reveal that 3E1, with both heavy and light chains, binds to a conserved epitope of the HA stem region, comprising parts of the fusion peptide, the F subdomain and the outermost beta-strand preceding helix A. Altogether, these data suggest the potential of 3E1 as a therapeutic drug against H1 and H5 subtype viruses.
		+
		+	Human antibody 3E1 targets the HA stem region of H1N1 and H5N6 influenza A viruses.,Wang W, Sun X, Li Y, Su J, Ling Z, Zhang T, Wang F, Zhang H, Chen H, Ding J, Sun B Nat Commun. 2016 Dec 2;7:13577. doi: 10.1038/ncomms13577. PMID:27910950<ref>PMID:27910950</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gjt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:12, 11 December 2016

OCA — Sun, 11 Dec 2016 02:12:00 GMT

←Older revision		Revision as of 02:12, 11 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5gjt is ON HOLD until Paper Publication~~	+	==Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1==
-		+	<StructureSection load='5gjt' size='340' side='right' caption='[[5gjt]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~Authors: Wang, W., Zhang, T., Ding, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gjt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GJT FirstGlance]. <br>
-	~~Description:~~ Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1	+	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gjs\|5gjs]]</td></tr>
-	[[~~Category~~: ~~Zhang~~, T]]	+	<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=5gjt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjt OCA], [http://pdbe.org/5gjt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjt RCSB], [http://www.ebi.ac.uk/pdbsum/5gjt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjt ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/N0C8E5_9INFA N0C8E5_9INFA]] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.[RuleBase:RU003324][SAAS:SAAS00363335]
		+	__TOC__
		+	</StructureSection>
	[[Category: Ding, J]]		[[Category: Ding, J]]
	[[Category: Wang, W]]		[[Category: Wang, W]]
		+	[[Category: Zhang, T]]
		+	[[Category: Complementarity determining region]]
		+	[[Category: Epitope]]
		+	[[Category: Fab]]
		+	[[Category: Immune system]]
		+	[[Category: Paratope]]

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

OCA — Thu, 14 Jul 2016 06:35:39 GMT

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

←Older revision

Revision as of 06:35, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gjt is ON HOLD until Paper Publication Authors: Wang, W., Zhang, T., Ding, J. Description: Crystal structure of H1 hemagglutinin from A/Washington...

OCA — Thu, 14 Jul 2016 06:35:38 GMT

New page: '''Unreleased structure''' The entry 5gjt is ON HOLD until Paper Publication Authors: Wang, W., Zhang, T., Ding, J. Description: Crystal structure of H1 hemagglutinin from A/Washington...

New page

'''Unreleased structure'''

The entry 5gjt is ON HOLD until Paper Publication

Authors: Wang, W., Zhang, T., Ding, J.

Description: Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1
[[Category: Unreleased Structures]]
[[Category: Zhang, T]]
[[Category: Ding, J]]
[[Category: Wang, W]]