2fx9 - Revision history

OCA at 09:32, 30 August 2023

OCA — Wed, 30 Aug 2023 09:32:51 GMT

←Older revision		Revision as of 09:32, 30 August 2023
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	<StructureSection load='2fx9' size='340' side='right'caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2fx9' size='340' side='right'caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(WMJ2_ISOLATE) Human immunodeficiency virus type 1 (WMJ2 ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ORQ:N~5~~~-~~ACETYL-L-ORNITHINE'>ORQ</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [https://pdbe.org/2fx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2fx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fx9 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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [https://pdbe.org/2fx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2fx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fx9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ENV_HV1W2 ENV_HV1W2] The surface protein gp120 (SU) attaches the virus to the host lymphoid cell by binding to the primary receptor CD4. This interaction induces a structural rearrangement creating a high affinity binding site for a chemokine coreceptor like CXCR4 and/or CCR5. This peculiar 2 stage receptor-interaction strategy allows gp120 to maintain the highly conserved coreceptor-binding site in a cryptic conformation, protected from neutralizing antibodies. Since CD4 also displays a binding site for the disulfide-isomerase P4HB/PDI, a P4HB/PDI-CD4-CXCR4-gp120 complex may form. In that complex, P4HB/PDI could reach and reduce gp120 disulfide bonds, causing major conformational changes in gp120. TXN, another PDI family member could also be involved in disulfide rearrangements in Env during fusion. These changes are transmitted to the transmembrane protein gp41 and are thought to activate its fusogenic potential by unmasking its fusion peptide. Surface protein gp120 (SU) may target the virus to gut-associated lymphoid tissue (GALT) by binding host ITGA4/ITGB7 (alpha-4/beta-7 integrins), a complex that mediates T-cell migration to the GALT. Interaction between gp120 and ITGA4/ITGB7 would allow the virus to enter GALT early in the infection, infecting and killing most of GALT's resting CD4+ T-cells. This T-cell depletion is believed to be the major insult to the host immune system leading to AIDS (By similarity). The surface protein gp120 is a ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses. These interactions allow capture of viral particles at mucosal surfaces by these cells and subsequent transmission to permissive cells. DCs are professional antigen presenting cells, critical for host immunity by inducing specific immune responses against a broad variety of pathogens. They act as sentinels in various tissues where they take up antigen, process it, and present it to T-cells following migration to lymphoid organs. HIV subverts the migration properties of dendritic cells to gain access to CD4+ T-cells in lymph nodes. Virus transmission to permissive T-cells occurs either in trans (without DCs infection, through viral capture and transmission), or in cis (following DCs productive infection, through the usual CD4-gp120 interaction), thereby inducing a robust infection. In trans infection, bound virions remain infectious over days and it is proposed that they are not degraded, but protected in non-lysosomal acidic organelles within the DCs close to the cell membrane thus contributing to the viral infectious potential during DCs' migration from the periphery to the lymphoid tissues. On arrival at lymphoid tissues, intact virions recycle back to DCs' cell surface allowing virus transmission to CD4+ T-cells. Virion capture also seems to lead to MHC-II-restricted viral antigen presentation, and probably to the activation of HIV-specific CD4+ cells (By similarity). The transmembrane protein gp41 (TM) acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of viral and target intracellular membranes, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Complete fusion occurs in host cell endosomes and is dynamin-dependent, however some lipid transfer might occur at the plasma membrane. The virus undergoes clathrin-dependent internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm (By similarity). The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface (By similarity). The gp120-gp41 heterodimer seems to contribute to T-cell depletion during HIV-1 infection. The envelope glycoproteins expressed on the surface of infected cells induce apoptosis through an interaction with uninfected cells expressing the receptor (CD4) and the coreceptors CXCR4 or CCR5. This type of bystander killing may be obtained by at least three distinct mechanisms. First, the interaction between the 2 cells can induce cellular fusion followed by nuclear fusion within the syncytium. Syncytia are condemned to die from apoptosis. Second, the 2 interacting cells may not fuse entirely and simply exchange plasma membrane lipids, after a sort of hemifusion process, followed by rapid death. Third, it is possible that virus-infected cells, on the point of undergoing apoptosis, fuse with CD4-expressing cells, in which case apoptosis is rapidly transmitted from one cell to the other and thus occurs in a sort of contagious fashion (By similarity). The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brunel~~, F M~~]]	+	[[Category: Brunel FM]]
-	[[Category: Burton~~, D R~~]]	+	[[Category: Burton DR]]
-	[[Category: Cardoso~~, R M.F~~]]	+	[[Category: Cardoso RMF]]
-	[[Category: Dawson~~, P E~~]]	+	[[Category: Dawson PE]]
-	[[Category: Ferguson, S]]	+	[[Category: Ferguson S]]
-	[[Category: Wilson~~, I A]]~~	+	[[Category: Wilson IA]]
-	~~[[Category: Antibody-epitope complex]]~~	+
-	~~[[Category: Beta-sandwich]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin fold~~]]	+

OCA at 14:37, 29 December 2021

OCA — Wed, 29 Dec 2021 14:37:59 GMT

←Older revision		Revision as of 14:37, 29 December 2021
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	<StructureSection load='2fx9' size='340' side='right'caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2fx9' size='340' side='right'caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</div></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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [~~http~~://pdbe.org/2fx9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fx9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fx9 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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [https://pdbe.org/2fx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2fx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:06, 27 March 2020

OCA — Fri, 27 Mar 2020 11:06:37 GMT

←Older revision		Revision as of 11:06, 27 March 2020
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	==Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41==		==Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41==
-	<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2fx9' size='340' side='right'caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Brunel, F M]]		[[Category: Brunel, F M]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 06:42, 20 June 2018

OCA — Wed, 20 Jun 2018 06:42:57 GMT

←Older revision		Revision as of 06:42, 20 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41==		==Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41==
	<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://pdbe.org/2fx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://pdbe.org/2fx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fx/2fx9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fx/2fx9_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	==See Also==		==See Also==
-	*[[Antibody\|Antibody]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:12, 7 February 2016

OCA — Sun, 07 Feb 2016 14:12:19 GMT

←Older revision		Revision as of 14:12, 7 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fx9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:16, 10 September 2015

OCA — Thu, 10 Sep 2015 02:16:00 GMT

←Older revision		Revision as of 02:16, 10 September 2015
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	<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://pdbe.org/2fx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2fx9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Brunel, F M]]		[[Category: Brunel, F M]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 07:56, 16 January 2015

OCA — Fri, 16 Jan 2015 07:56:20 GMT

←Older revision		Revision as of 07:56, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</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=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Brunel, F M.]]	+	[[Category: Brunel, F M]]
-	[[Category: Burton, D R.]]	+	[[Category: Burton, D R]]
-	[[Category: Cardoso, R M.F.]]	+	[[Category: Cardoso, R M.F]]
-	[[Category: Dawson, P E.]]	+	[[Category: Dawson, P E]]
-	[[Category: Ferguson, S.]]	+	[[Category: Ferguson, S]]
-	[[Category: Wilson, I A.]]	+	[[Category: Wilson, I A]]
	[[Category: Antibody-epitope complex]]		[[Category: Antibody-epitope complex]]
	[[Category: Beta-sandwich]]		[[Category: Beta-sandwich]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Immunoglobulin fold]]		[[Category: Immunoglobulin fold]]

OCA at 05:28, 29 September 2014

OCA — Mon, 29 Sep 2014 05:28:52 GMT

←Older revision		Revision as of 05:28, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2fx9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41==
		+	<StructureSection load='2fx9' size='340' side='right' caption='[[2fx9]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FX9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORQ:N~5~-ACETYL-L-ORNITHINE'>ORQ</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzg\|1tzg]], [[2fx7\|2fx7]], [[2fx8\|2fx8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2fx9 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fx/2fx9_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Potent, broadly HIV-1 neutralizing antibodies (nAbs) may be invaluable for the design of an AIDS vaccine. 4E10 is the broadest HIV-1 nAb known to date and recognizes a contiguous and highly conserved helical epitope in the membrane-proximal region of gp41. The 4E10 epitope is thus an excellent target for vaccine design as it is also highly amenable to peptide engineering to enhance its helical character. To investigate the structural effect of both increasing the peptide length and of introducing helix-promoting constraints in the 4E10 epitope, we have determined crystal structures of Fab 4E10 bound to an optimized peptide epitope (NWFDITNWLWYIKKKK-NH(2)), an Aib-constrained peptide epitope (NWFDITNAibLWRR-NH(2)), and a thioether-linked peptide (NWFCITOWLWKKKK-NH(2)) to resolutions of 1.7 A, 2.1 A, and 2.2 A, respectively. The thioether-linked peptide is the first reported structure of a cyclic tethered helical peptide bound to an antibody. The introduced helix constraints limit the conformational flexibility of the peptides without affecting interactions with 4E10. The substantial increase in affinity (10 nM versus 10(4) nM of the IC(50) of the original KGND peptide template) is largely realized by 4E10 interaction with an additional helical turn at the peptide C terminus that includes Leu679 and Trp680. Thus, the core 4E10 epitope was extended and modified to a WFX(I/L)(T/S)XX(L/I)W motif, where X does not play a major role in 4E10 binding and can be used to introduce helical-promoting constraints in the peptide epitope.

-	~~{{STRUCTURE_2fx9\| PDB=2fx9 \| SCENE= }}~~	+	Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10.,Cardoso RM, Brunel FM, Ferguson S, Zwick M, Burton DR, Dawson PE, Wilson IA J Mol Biol. 2007 Feb 2;365(5):1533-44. Epub 2006 Nov 10. PMID:17125793<ref>PMID:17125793</ref>

-	~~===Crystal structure~~ of ~~hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing~~ the ~~4e10 epitope on gp41===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17125793}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2fx9]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA].~~	+

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017125793<~~/~~ref~~><~~ref group="xtra">PMID:015723805</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Brunel, F M.]]		[[Category: Brunel, F M.]]

OCA at 06:53, 20 October 2012

OCA — Sat, 20 Oct 2012 06:53:11 GMT

←Older revision		Revision as of 06:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2fx9]] is a 6 chain structure ~~of [[Antibody]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA].	+	[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA].

	==See Also==		==See Also==

OCA at 14:38, 25 July 2012

OCA — Wed, 25 Jul 2012 14:38:00 GMT

←Older revision		Revision as of 14:38, 25 July 2012
Line 1:		Line 1:
	[[Image:2fx9.png\|left\|200px]]		[[Image:2fx9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2fx9", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2fx9\| PDB=2fx9 \| SCENE= }}		{{STRUCTURE_2fx9\| PDB=2fx9 \| SCENE= }}

	===Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41===		===Crystal structure of hiv-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17125793}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17125793 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17125793}}		{{ABSTRACT_PUBMED_17125793}}

	==About this Structure==		==About this Structure==
-	[[2fx9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA].	+	[[2fx9]] is a 6 chain structure of [[Antibody]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FX9 OCA].
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17125793~~</ref><ref group="xtra">PMID:~~15723805~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017125793</ref><ref group="xtra">PMID:015723805</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Brunel, F M.]]		[[Category: Brunel, F M.]]