3idx - Revision history

OCA at 07:44, 6 September 2023

2023-09-06T07:44:55Z

←Older revision		Revision as of 07:44, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3idx' size='340' side='right'caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3idx' size='340' side='right'caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~] and [https://en.wikipedia.org/wiki/Human ~~Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3idy\|3idy]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [https://pdbe.org/3idx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [https://www.ebi.ac.uk/pdbsum/3idx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idx 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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [https://pdbe.org/3idx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [https://www.ebi.ac.uk/pdbsum/3idx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ENV_HV1H2 ENV_HV1H2] 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.<ref>PMID:19410541</ref> 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).<ref>PMID:19410541</ref> 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.<ref>PMID:19410541</ref> 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.<ref>PMID:19410541</ref> 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).<ref>PMID:19410541</ref> 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.<ref>PMID:19410541</ref> 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.<ref>PMID:19410541</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arthos, J]]	+	[[Category: Arthos J]]
-	[[Category: Burton~~, D R~~]]	+	[[Category: Burton DR]]
-	[[Category: Cavacini, L]]	+	[[Category: Cavacini L]]
-	[[Category: Chen, L]]	+	[[Category: Chen L]]
-	[[Category: ~~Dell, S O~~]]	+	[[Category: Dimitrov DS]]
-	[[Category: ~~Dimitrov, D S~~]]	+	[[Category: Hessell AJ]]
-	[[Category: ~~Hessell, A J~~]]	+	[[Category: Kwon YD]]
-	[[Category: ~~Kwon, Y D~~]]	+	[[Category: Kwong PD]]
-	[[Category: ~~Kwong, P D~~]]	+	[[Category: Mascola JR]]
-	[[Category: ~~Mascola, J R~~]]	+	[[Category: Nabel GJ]]
-	[[Category: ~~Nabel, G J~~]]	+	[[Category: O'Dell S]]
-	[[Category: Pancera, M]]	+	[[Category: Pancera M]]
-	[[Category: Posner, M]]	+	[[Category: Posner M]]
-	[[Category: Sodroski, J]]	+	[[Category: Sodroski J]]
-	[[Category: Tang, M]]	+	[[Category: Tang M]]
-	[[Category: Wu, X]]	+	[[Category: Wu X]]
-	[[Category: Wyatt, R]]	+	[[Category: Wyatt R]]
-	[[Category: Xu, L]]	+	[[Category: Xu L]]
-	[[Category: Yang~~, Z Y~~]]	+	[[Category: Yang ZY]]
-	[[Category: Zhang~~, M Y~~]]	+	[[Category: Zhang MY]]
-	[[Category: Zhou, T]]	+	[[Category: Zhou T]]
-	~~[[Category: Aid]]~~	+
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Apoptosis]]~~	+
-	~~[[Category: B13]]~~	+
-	~~[[Category: Cd4-binding site]]~~	+
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Cleavage on pair of basic residue]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Envelope glycan protein]]~~	+
-	~~[[Category: Envelope protein]]~~	+
-	~~[[Category: Fusion protein]]~~	+
-	~~[[Category: Gp120]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Host-virus interaction]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Viral immunoevasion]]~~	+
-	~~[[Category: Virion~~]]	+

OCA at 10:36, 31 March 2021

2021-03-31T10:36:32Z

←Older revision		Revision as of 10:36, 31 March 2021
Line 1:		Line 1:

	==Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222==		==Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222==
-	<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3idx' size='340' side='right'caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/9hiv1 9hiv1] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IDX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3idy\|3idy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [~~http~~://pdbe.org/3idx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3idx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3idx 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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [https://pdbe.org/3idx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [https://www.ebi.ac.uk/pdbsum/3idx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3idx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
-	*[[Gp120\|Gp120]]	+	*[[Gp120 3D structures\|Gp120 3D structures]]
		+	*[[3D structures of human antibody\|3D structures of human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arthos, J]]		[[Category: Arthos, J]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 09:31, 19 December 2018

2018-12-19T09:31:52Z

←Older revision		Revision as of 09:31, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222==		==Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222==
	<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [http://pdbe.org/3idx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [http://www.ebi.ac.uk/pdbsum/3idx 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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [http://pdbe.org/3idx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [http://www.ebi.ac.uk/pdbsum/3idx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3idx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/3idx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/3idx_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>
Line 29:		Line 30:

	==See Also==		==See Also==
-	*[[Antibody\|Antibody]]	+	*[[Antibody 3D structures\|Antibody 3D structures]]
	*[[Gp120\|Gp120]]		*[[Gp120\|Gp120]]
	== References ==		== References ==

OCA at 05:51, 9 February 2016

2016-02-09T05:51:13Z

←Older revision		Revision as of 05:51, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~] and [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_1~~ Human ~~immunodeficiency virus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 ~~Human immunodeficiency virus 1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [http://www.ebi.ac.uk/pdbsum/3idx 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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [http://pdbe.org/3idx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [http://www.ebi.ac.uk/pdbsum/3idx PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3idx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3idx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Homo sapiens]]~~	+	[[Category: Human]]
-	[[Category: Human ~~immunodeficiency virus 1~~]]	+
	[[Category: Arthos, J]]		[[Category: Arthos, J]]
	[[Category: Burton, D R]]		[[Category: Burton, D R]]

OCA at 06:26, 18 December 2014

2014-12-18T06:26:54Z

←Older revision		Revision as of 06:26, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3idx\| PDB=3idx \| SCENE= }}~~	+	==Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222==
-	===Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222===	+	<StructureSection load='3idx' size='340' side='right' caption='[[3idx]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19965434}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3idx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IDX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3idy\|3idy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</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=3idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3idx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3idx RCSB], [http://www.ebi.ac.uk/pdbsum/3idx 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/id/3idx_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 ==
		+	The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two poorly neutralizing, CD4-binding site (CD4BS) antibodies, F105 and b13, in complexes with gp120. Both antibodies exhibited approach angles to gp120 similar to those of CD4 and a rare, broadly neutralizing CD4BS antibody, b12. Slight differences in recognition, however, resulted in substantial differences in F105- and b13-bound conformations relative to b12-bound gp120. Modeling and binding experiments revealed these conformations to be poorly compatible with the viral spike. This incompatibility, the consequence of slight differences in CD4BS recognition, renders HIV-1 resistant to all but the most accurately targeted antibodies.

-	~~==About this Structure==~~	+	Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120.,Chen L, Do Kwon Y, Zhou T, Wu X, O'Dell S, Cavacini L, Hessell AJ, Pancera M, Tang M, Xu L, Yang ZY, Zhang MY, Arthos J, Burton DR, Dimitrov DS, Nabel GJ, Posner MR, Sodroski J, Wyatt R, Mascola JR, Kwong PD Science. 2009 Nov 20;326(5956):1123-7. PMID:19965434<ref>PMID:19965434</ref>
-	~~[[3idx]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens] and [http~~:~~//en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3IDX OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
	*[[Gp120\|Gp120]]		*[[Gp120\|Gp120]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019965434<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Arthos, J.]]	+	[[Category: Arthos, J]]
-	[[Category: Burton, D R.]]	+	[[Category: Burton, D R]]
-	[[Category: Cavacini, L.]]	+	[[Category: Cavacini, L]]
-	[[Category: Chen, L.]]	+	[[Category: Chen, L]]
-	[[Category: Dell, S O.]]	+	[[Category: Dell, S O]]
-	[[Category: Dimitrov, D S.]]	+	[[Category: Dimitrov, D S]]
-	[[Category: Hessell, A J.]]	+	[[Category: Hessell, A J]]
-	[[Category: Kwon, Y D.]]	+	[[Category: Kwon, Y D]]
-	[[Category: Kwong, P D.]]	+	[[Category: Kwong, P D]]
-	[[Category: Mascola, J R.]]	+	[[Category: Mascola, J R]]
-	[[Category: Nabel, G J.]]	+	[[Category: Nabel, G J]]
-	[[Category: Pancera, M.]]	+	[[Category: Pancera, M]]
-	[[Category: Posner, M.]]	+	[[Category: Posner, M]]
-	[[Category: Sodroski, J.]]	+	[[Category: Sodroski, J]]
-	[[Category: Tang, M.]]	+	[[Category: Tang, M]]
-	[[Category: Wu, X.]]	+	[[Category: Wu, X]]
-	[[Category: Wyatt, R.]]	+	[[Category: Wyatt, R]]
-	[[Category: Xu, L.]]	+	[[Category: Xu, L]]
-	[[Category: Yang, Z Y.]]	+	[[Category: Yang, Z Y]]
-	[[Category: Zhang, M Y.]]	+	[[Category: Zhang, M Y]]
-	[[Category: Zhou, T.]]	+	[[Category: Zhou, T]]
	[[Category: Aid]]		[[Category: Aid]]
	[[Category: Antibody]]		[[Category: Antibody]]

OCA at 09:15, 11 March 2013

2013-03-11T09:15:16Z

←Older revision		Revision as of 09:15, 11 March 2013
Line 1:		Line 1:
-	[[Image:3idx.png\|left\|200px]]
-
	{{STRUCTURE_3idx\| PDB=3idx \| SCENE= }}		{{STRUCTURE_3idx\| PDB=3idx \| SCENE= }}
-
	===Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222===		===Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222===
-
	{{ABSTRACT_PUBMED_19965434}}		{{ABSTRACT_PUBMED_19965434}}

OCA at 12:51, 20 October 2012

2012-10-20T12:51:38Z

←Older revision		Revision as of 12:51, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3idx]] is a 3 chain structure ~~of [[Antibody]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].	+	[[3idx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
		+	*[[Gp120\|Gp120]]

	==Reference==		==Reference==

OCA: Protected "3idx" [edit=sysop:move=sysop]

2012-07-26T10:06:59Z

Protected "3idx" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:06, 26 July 2012

OCA at 10:06, 26 July 2012

2012-07-26T10:06:56Z

←Older revision		Revision as of 10:06, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3idx.png\|left\|200px]]		[[Image:3idx.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3idx", 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_3idx\| PDB=3idx \| SCENE= }}		{{STRUCTURE_3idx\| PDB=3idx \| SCENE= }}

	===Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222===		===Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19965434}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19965434 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19965434}}		{{ABSTRACT_PUBMED_19965434}}

	==About this Structure==		==About this Structure==
-	~~3IDX~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].	+	[[3idx]] is a 3 chain structure of [[Antibody]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19965434~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019965434</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
Line 54:		Line 45:
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Cleavage on pair of basic residue]]		[[Category: Cleavage on pair of basic residue]]
-	[[Category: Coiled coil]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
	[[Category: Envelope glycan protein]]		[[Category: Envelope glycan protein]]
Line 67:		Line 57:
	[[Category: Viral immunoevasion]]		[[Category: Viral immunoevasion]]
	[[Category: Virion]]		[[Category: Virion]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:51:19 2010''

OCA at 12:51, 28 January 2010

2010-01-28T12:51:19Z

←Older revision		Revision as of 12:51, 28 January 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3IDX is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].	+	3IDX is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IDX OCA].

	==Reference==		==Reference==
Line 68:		Line 68:
	[[Category: Virion]]		[[Category: Virion]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Dec 24 07:~~28:~~56 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:51:19 2010''