6d0u - Revision history

OCA at 15:15, 4 October 2023

OCA — Wed, 04 Oct 2023 15:15:32 GMT

←Older revision		Revision as of 15:15, 4 October 2023
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	<StructureSection load='6d0u' size='340' side='right'caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>		<StructureSection load='6d0u' size='340' side='right'caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~I68a4 I68a4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Hong_Kong/1/1968(H3N2)) Influenza A virus (A/Hong Kong/1/1968(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D0U 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]] 3.25Å</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=506350 I68A4])~~</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='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=6d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0u OCA], [~~http~~://pdbe.org/6d0u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d0u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d0u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0u 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=6d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0u OCA], [https://pdbe.org/6d0u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d0u RCSB], [https://www.ebi.ac.uk/pdbsum/6d0u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HEMA_I68A4 HEMA_I68A4]] 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 (By similarity).	+	[https://www.uniprot.org/uniprot/HEMA_I68A4 HEMA_I68A4] 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 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Hemagglutinin 3D structures\|Hemagglutinin 3D structures]]		*[[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: I68a4~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wilson~~, I A~~]]	+	[[Category: Wilson IA]]
-	[[Category: Wu~~, N C]]~~	+	[[Category: Wu NC]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Antiviral protein]]~~	+
-	~~[[Category: Computational design]]~~	+
-	~~[[Category: Hemagglutinin]]~~	+
-	~~[[Category: Influenza~~]]	+

OCA at 09:54, 18 December 2019

OCA — Wed, 18 Dec 2019 09:54:28 GMT

←Older revision		Revision as of 09:54, 18 December 2019
Line 1:		Line 1:

	==Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1 subunit==		==Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1 subunit==
-	<StructureSection load='6d0u' size='340' side='right' caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>	+	<StructureSection load='6d0u' size='340' side='right'caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/I68a4 I68a4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0U FirstGlance]. <br>		<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/I68a4 I68a4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0U FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6d0u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6d0u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Hemagglutinin 3D structures\|Hemagglutinin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 29:
	[[Category: Human]]		[[Category: Human]]
	[[Category: I68a4]]		[[Category: I68a4]]
		+	[[Category: Large Structures]]
	[[Category: Wilson, I A]]		[[Category: Wilson, I A]]
	[[Category: Wu, N C]]		[[Category: Wu, N C]]

OCA at 09:26, 30 January 2019

OCA — Wed, 30 Jan 2019 09:26:16 GMT

←Older revision		Revision as of 09:26, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='6d0u' size='340' side='right' caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>		<StructureSection load='6d0u' size='340' side='right' caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/I68a4 I68a4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0U 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='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=506350 I68A4])</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=6d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0u OCA], [http://pdbe.org/6d0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d0u RCSB], [http://www.ebi.ac.uk/pdbsum/6d0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0u 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=6d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0u OCA], [http://pdbe.org/6d0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d0u RCSB], [http://www.ebi.ac.uk/pdbsum/6d0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/HEMA_I68A4 HEMA_I68A4]] 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 (By similarity).		[[http://www.uniprot.org/uniprot/HEMA_I68A4 HEMA_I68A4]] 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 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Influenza is a yearly threat to global public health. Rapid changes in influenza surface proteins resulting from antigenic drift and shift events make it difficult to readily identify antibodies with broadly neutralizing activity against different influenza subtypes with high frequency, specifically antibodies targeting the receptor binding domain (RBD) on influenza HA protein. We developed an optimized computational design method that is able to optimize an antibody for recognition of large panels of antigens. To demonstrate the utility of this multistate design method, we used it to redesign an antiinfluenza antibody against a large panel of more than 500 seasonal HA antigens of the H1 subtype. As a proof of concept, we tested this method on a variety of known antiinfluenza antibodies and identified those that could be improved computationally. We generated redesigned variants of antibody C05 to the HA RBD and experimentally characterized variants that exhibited improved breadth and affinity against our panel. C05 mutants exhibited improved affinity for three of the subtypes used in design by stabilizing the CDRH3 loop and creating favorable electrostatic interactions with the antigen. These mutants possess increased breadth and affinity of binding while maintaining high-affinity binding to existing targets, surpassing a major limitation up to this point.
		+
		+	Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses.,Sevy AM, Wu NC, Gilchuk IM, Parrish EH, Burger S, Yousif D, Nagel MBM, Schey KL, Wilson IA, Crowe JE Jr, Meiler J Proc Natl Acad Sci U S A. 2019 Jan 14. pii: 1806004116. doi:, 10.1073/pnas.1806004116. PMID:30642961<ref>PMID:30642961</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6d0u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: I68a4]]
	[[Category: Wilson, I A]]		[[Category: Wilson, I A]]
	[[Category: Wu, N C]]		[[Category: Wu, N C]]

OCA at 12:06, 16 January 2019

OCA — Wed, 16 Jan 2019 12:06:11 GMT

←Older revision		Revision as of 12:06, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6d0u is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1 subunit==
-		+	<StructureSection load='6d0u' size='340' side='right' caption='[[6d0u]], [[Resolution\|resolution]] 3.25Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6d0u]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D0U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D0U FirstGlance]. <br>
-	~~Description~~:	+	</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='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=6d0u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d0u OCA], [http://pdbe.org/6d0u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d0u RCSB], [http://www.ebi.ac.uk/pdbsum/6d0u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d0u ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HEMA_I68A4 HEMA_I68A4]] 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 (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wilson, I A]]
		+	[[Category: Wu, N C]]
		+	[[Category: Antibody]]
		+	[[Category: Antiviral protein]]
		+	[[Category: Computational design]]
		+	[[Category: Hemagglutinin]]
		+	[[Category: Influenza]]

OCA at 06:40, 2 May 2018

OCA — Wed, 02 May 2018 06:40:25 GMT

←Older revision		Revision as of 06:40, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6d0u is ON HOLD	+	The entry 6d0u is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6d0u" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2018 04:19:37 GMT

Protected "6d0u" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6d0u is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Apr 2018 04:19:35 GMT

New page: '''Unreleased structure''' The entry 6d0u is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6d0u is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]