5ujz - Revision history

OCA at 21:54, 10 April 2020

OCA — Fri, 10 Apr 2020 21:54:57 GMT

←Older revision		Revision as of 21:54, 10 April 2020
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	<SX load='5ujz' size='340' side='right' viewer='molstar' caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>		<SX load='5ujz' size='340' side='right' viewer='molstar' caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/solomon_islands/03/2006(h1n1)) Influenza a virus (a/solomon islands/03/2006(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/solomon_islands/03/2006(h1n1)) Influenza a virus (a/solomon islands/03/2006(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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">[[5uk0\|5uk0]], [[5uk1\|5uk1]], [[5uk2\|5uk2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uk0\|5uk0]], [[5uk1\|5uk1]], [[5uk2\|5uk2]]</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=464623 Influenza A virus (A/Solomon Islands/03/2006(H1N1))])</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=464623 Influenza A virus (A/Solomon Islands/03/2006(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=5ujz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujz OCA], [http://pdbe.org/5ujz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujz RCSB], [http://www.ebi.ac.uk/pdbsum/5ujz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujz ProSAT]</span></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=5ujz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujz OCA], [http://pdbe.org/5ujz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujz RCSB], [http://www.ebi.ac.uk/pdbsum/5ujz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:43, 6 March 2020

OCA — Fri, 06 Mar 2020 19:43:20 GMT

←Older revision		Revision as of 19:43, 6 March 2020
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	==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1==		==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1==
-	<~~StructureSection~~ load='5ujz' size='340' side='right'caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>	+	<SX load='5ujz' size='340' side='right' viewer='molstar' caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/solomon_islands/03/2006(h1n1)) Influenza a virus (a/solomon islands/03/2006(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/solomon_islands/03/2006(h1n1)) Influenza a virus (a/solomon islands/03/2006(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>
Line 28:		Line 28:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Human]]		[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 17:08, 11 December 2019

OCA — Wed, 11 Dec 2019 17:08:35 GMT

←Older revision		Revision as of 17:08, 11 December 2019
Line 1:		Line 1:

	==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1==		==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1==
-	<StructureSection load='5ujz' size='340' side='right' caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>	+	<StructureSection load='5ujz' size='340' side='right'caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Influenza_a_virus_(a/solomon_islands/03/2006(h1n1)) Influenza a virus (a/solomon islands/03/2006(h1n1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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=BMA:BETA-D-MANNOSE'>BMA</scene>, <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">[[5uk0\|5uk0]], [[5uk1\|5uk1]], [[5uk2\|5uk2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uk0\|5uk0]], [[5uk1\|5uk1]], [[5uk2\|5uk2]]</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=464623 Influenza A virus (A/Solomon Islands/03/2006(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=5ujz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujz OCA], [http://pdbe.org/5ujz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujz RCSB], [http://www.ebi.ac.uk/pdbsum/5ujz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujz 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=5ujz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujz OCA], [http://pdbe.org/5ujz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujz RCSB], [http://www.ebi.ac.uk/pdbsum/5ujz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujz ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5ujz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ujz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Hemagglutinin 3D structures\|Hemagglutinin 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Caradonna, T]]		[[Category: Caradonna, T]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]

OCA at 09:21, 3 August 2017

OCA — Thu, 03 Aug 2017 09:21:29 GMT

←Older revision		Revision as of 09:21, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ujz is ~~ON HOLD~~	+	==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 1==
		+	<StructureSection load='5ujz' size='340' side='right' caption='[[5ujz]], [[Resolution\|resolution]] 4.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ujz]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UJZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <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">[[5uk0\|5uk0]], [[5uk1\|5uk1]], [[5uk2\|5uk2]]</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=5ujz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ujz OCA], [http://pdbe.org/5ujz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ujz RCSB], [http://www.ebi.ac.uk/pdbsum/5ujz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ujz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A7UPX0_9INFA A7UPX0_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:SAAS00145386]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines.The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen-antibody interface, although small variation in the twist of the rod-likeHA trimer limited the overall resolution to about 4.5A.Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results.The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.

-	~~Authors:~~ Liu, Y., Pan, J., ~~Caradonna~~, T., ~~Jenni~~, S., ~~Rayond~~, D.D.~~, Schmidt, A~~.G.~~, Harrison, S~~.C., ~~Grigorieff, N~~.	+	CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface.,Liu Y, Pan J, Jenni S, Raymond DD, Caradonna T, Do KT, Schmidt AG, Harrison SC, Grigorieff N J Mol Biol. 2017 Jun 16;429(12):1829-1839. doi: 10.1016/j.jmb.2017.05.011. Epub, 2017 May 12. PMID:28506635<ref>PMID:28506635</ref>

-	~~Description: CryoEM structure~~ of ~~an influenza virus receptor-binding site antibody~~-~~antigen interface~~ -~~Class 1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Harrison~~, ~~S.C~~]]	+	<div class="pdbe-citations 5ujz" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Rayond~~, ~~D.D~~]]	+	== References ==
-	[[Category: ~~Liu~~, Y]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Caradonna, T]]
		+	[[Category: Grigorieff, N]]
		+	[[Category: Harrison, S C]]
	[[Category: Jenni, S]]		[[Category: Jenni, S]]
		+	[[Category: Liu, Y]]
	[[Category: Pan, J]]		[[Category: Pan, J]]
-	[[Category: ~~Grigorieff~~, N]]	+	[[Category: Raymond, D D]]
-	[[Category: Schmidt, A.G]]	+	[[Category: Schmidt, A G]]
-	[[Category: ~~Caradonna, T~~]]	+	[[Category: Antibody fragment]]
		+	[[Category: Hemagglutinin]]
		+	[[Category: Viral glycoprotein]]
		+	[[Category: Viral protein-immune system complex]]

OCA at 10:34, 4 May 2017

OCA — Thu, 04 May 2017 10:34:55 GMT

←Older revision		Revision as of 10:34, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ujz is ON HOLD ~~until Paper Publication~~	+	The entry 5ujz is ON HOLD

	Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.		Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.

OCA at 19:07, 15 March 2017

OCA — Wed, 15 Mar 2017 19:07:07 GMT

←Older revision		Revision as of 19:07, 15 March 2017
Line 7:		Line 7:
	Description: CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface -Class 1		Description: CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface -Class 1
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Harrison, S.C]]
	[[Category: Rayond, D.D]]		[[Category: Rayond, D.D]]
	[[Category: Liu, Y]]		[[Category: Liu, Y]]
-	[[Category: Grigorieff, N]]
-	[[Category: Schmidt, A.G]]
-	[[Category: Harrison, S.C]]
	[[Category: Jenni, S]]		[[Category: Jenni, S]]
	[[Category: Pan, J]]		[[Category: Pan, J]]
		+	[[Category: Grigorieff, N]]
		+	[[Category: Schmidt, A.G]]
	[[Category: Caradonna, T]]		[[Category: Caradonna, T]]

OCA at 14:32, 9 March 2017

OCA — Thu, 09 Mar 2017 14:32:04 GMT

←Older revision		Revision as of 14:32, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ujz is ON HOLD	+	The entry 5ujz is ON HOLD until Paper Publication

	Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.		Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.

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

OCA — Wed, 25 Jan 2017 22:16:07 GMT

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

←Older revision

Revision as of 22:16, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ujz is ON HOLD Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N. Description: CryoE...

OCA — Wed, 25 Jan 2017 22:16:05 GMT

New page: '''Unreleased structure''' The entry 5ujz is ON HOLD Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N. Description: CryoE...

New page

'''Unreleased structure'''

The entry 5ujz is ON HOLD

Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.

Description: CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface -Class 1
[[Category: Unreleased Structures]]
[[Category: Rayond, D.D]]
[[Category: Liu, Y]]
[[Category: Grigorieff, N]]
[[Category: Schmidt, A.G]]
[[Category: Harrison, S.C]]
[[Category: Jenni, S]]
[[Category: Pan, J]]
[[Category: Caradonna, T]]