3tgq - Revision history

OCA at 13:28, 14 March 2024

OCA — Thu, 14 Mar 2024 13:28:04 GMT

←Older revision		Revision as of 13:28, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3tgq' size='340' side='right'caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='3tgq' size='340' side='right'caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tgq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TGQ FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [https://pdbe.org/3tgq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [https://www.ebi.ac.uk/pdbsum/3tgq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tgq 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [https://pdbe.org/3tgq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [https://www.ebi.ac.uk/pdbsum/3tgq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tgq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/ENV_HV1Y2 ENV_HV1Y2] 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).
-	The ~~HIV-1 envelope (Env) spike (~~gp120(3)~~/gp41(3)) undergoes considerable structural rearrangements to mediate~~ virus ~~entry into cells and~~ to ~~evade~~ the host ~~immune response. Engagement of CD4,~~ the primary ~~human~~ receptor~~, fixes~~ a ~~particular conformation~~ and ~~primes Env for entry~~. ~~The CD4~~-~~bound state, however, is prone~~ to ~~spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1~~ maintain ~~CD4~~-binding ~~capacity and regulate transitions to~~ the CD4-~~bound state? To define this mechanistically~~, ~~we determined crystal structures of unliganded core~~ gp120 ~~from HIV-1 clades B~~, C, and E. ~~Notably, all of these unliganded HIV-1 structures resembled~~ the ~~CD4~~-~~bound state. Conformational fixation with ligand selection and thermodynamic analysis of full~~-~~length and core gp120 interactions revealed~~ that ~~the tendency of HIV~~-1 gp120 to ~~adopt~~ the CD4-~~bound conformation was restrained by~~ the V1/V2- and V3-~~variable loops~~. ~~In parallel~~, ~~we determined the structure~~ of ~~core gp120~~ in ~~complex with the small molecule~~, ~~NBD-556~~, ~~which specifically recognizes~~ the CD4-~~bound conformation of gp120~~. ~~Neutralization by NBD~~-~~556 indicated that Env spikes on primary isolates rarely assume~~ the CD4-~~bound conformation spontaneously~~, ~~although they could do so when quaternary restraints were loosened~~. ~~Together~~, ~~the results suggest~~ that the CD4-~~bound conformation represents a "ground state" for the gp120 core~~, ~~with variable loop~~ and ~~quaternary interactions restraining unliganded gp120 from "snapping" into this conformation. A mechanism~~ of ~~control involving deformations in unliganded structure from a functionally critical state~~ (e.g., the ~~CD4~~-~~bound~~ state) ~~provides advantages~~ in ~~terms~~ of ~~HIV~~-~~1 Env structural diversity~~ and ~~resistance~~ to ~~antibodies~~ and ~~inhibitors, while maintaining elements essential for entry~~.	+
-		+
-	~~Unliganded~~ HIV-1 ~~gp120 core structures assume~~ the ~~CD4-bound conformation~~ with ~~regulation by quaternary interactions~~ and ~~variable loops~~.,~~Kwon YD~~, ~~Finzi A~~, ~~Wu X~~, ~~Dogo~~-~~Isonagie C~~, ~~Lee LK~~, ~~Moore LR, Schmidt SD~~, ~~Stuckey J, Yang Y, Zhou T, Zhu J~~, ~~Vicic DA, Debnath AK, Shapiro L, Bewley CA, Mascola JR, Sodroski JG, Kwong PD Proc Natl Acad Sci U S A~~. ~~2012 Apr 10;109~~(15)~~:5663~~-8. ~~Epub 2012 Mar 26. PMID:22451932<ref>PMID:22451932</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database~~ of the U.~~S. National Library~~ of ~~Medicine~~.~~<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tgq" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Gp120 3D structures\|Gp120 3D structures]]		*[[Gp120 3D structures\|Gp120 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kwon~~, Y D~~]]	+	[[Category: Kwon YD]]
-	[[Category: Kwong~~, P D]]~~	+	[[Category: Kwong PD]]
-	~~[[Category: Hiv-1 gp120]]~~	+
-	~~[[Category: Unliganded structure]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 16:57, 6 July 2022

OCA — Wed, 06 Jul 2022 16:57:17 GMT

←Older revision		Revision as of 16:57, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core==		==Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core==
-	<StructureSection load='3tgq' size='340' side='right' caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<StructureSection load='3tgq' size='340' side='right'caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tgq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tgq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TGQ 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" id="ligandDat"><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">[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 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">HIV-1 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [~~http~~://pdbe.org/3tgq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tgq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tgq 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [https://pdbe.org/3tgq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [https://www.ebi.ac.uk/pdbsum/3tgq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tgq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Gp120\|Gp120]]	+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kwon, Y D]]		[[Category: Kwon, Y D]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]

OCA at 17:24, 11 August 2016

OCA — Thu, 11 Aug 2016 17:24:15 GMT

←Older revision		Revision as of 17:24, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core==		==Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core==
	<StructureSection load='3tgq' size='340' side='right' caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='3tgq' size='340' side='right' caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tgq]] is a 4 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=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TGQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tgq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TGQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~9606 HUMAN~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [http://www.ebi.ac.uk/pdbsum/3tgq 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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [http://pdbe.org/3tgq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [http://www.ebi.ac.uk/pdbsum/3tgq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tgq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3tgq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]
	[[Category: Kwon, Y D]]		[[Category: Kwon, Y D]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]

OCA at 10:54, 4 January 2015

OCA — Sun, 04 Jan 2015 10:54:45 GMT

←Older revision		Revision as of 10:54, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3tgq\| PDB=3tgq \| SCENE= }}~~	+	==Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core==
-	===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===	+	<StructureSection load='3tgq' size='340' side='right' caption='[[3tgq]], [[Resolution\|resolution]] 3.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22451932}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tgq]] is a 4 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=3TGQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TGQ 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tgr\|3tgr]], [[3tgs\|3tgs]], [[3tgt\|3tgt]], [[3tih\|3tih]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3tgq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tgq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tgq RCSB], [http://www.ebi.ac.uk/pdbsum/3tgq PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The HIV-1 envelope (Env) spike (gp120(3)/gp41(3)) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation and primes Env for entry. The CD4-bound state, however, is prone to spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1 maintain CD4-binding capacity and regulate transitions to the CD4-bound state? To define this mechanistically, we determined crystal structures of unliganded core gp120 from HIV-1 clades B, C, and E. Notably, all of these unliganded HIV-1 structures resembled the CD4-bound state. Conformational fixation with ligand selection and thermodynamic analysis of full-length and core gp120 interactions revealed that the tendency of HIV-1 gp120 to adopt the CD4-bound conformation was restrained by the V1/V2- and V3-variable loops. In parallel, we determined the structure of core gp120 in complex with the small molecule, NBD-556, which specifically recognizes the CD4-bound conformation of gp120. Neutralization by NBD-556 indicated that Env spikes on primary isolates rarely assume the CD4-bound conformation spontaneously, although they could do so when quaternary restraints were loosened. Together, the results suggest that the CD4-bound conformation represents a "ground state" for the gp120 core, with variable loop and quaternary interactions restraining unliganded gp120 from "snapping" into this conformation. A mechanism of control involving deformations in unliganded structure from a functionally critical state (e.g., the CD4-bound state) provides advantages in terms of HIV-1 Env structural diversity and resistance to antibodies and inhibitors, while maintaining elements essential for entry.

-	~~==About this Structure==~~	+	Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.,Kwon YD, Finzi A, Wu X, Dogo-Isonagie C, Lee LK, Moore LR, Schmidt SD, Stuckey J, Yang Y, Zhou T, Zhu J, Vicic DA, Debnath AK, Shapiro L, Bewley CA, Mascola JR, Sodroski JG, Kwong PD Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5663-8. Epub 2012 Mar 26. PMID:22451932<ref>PMID:22451932</ref>
-	~~[[3tgq]] is a 4 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=3TGQ OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Gp120\|Gp120]]		*[[Gp120\|Gp120]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:022451932</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Kwon, Y D.]]	+	[[Category: Kwon, Y D]]
-	[[Category: Kwong, P D.]]	+	[[Category: Kwong, P D]]
	[[Category: Hiv-1 gp120]]		[[Category: Hiv-1 gp120]]
	[[Category: Unliganded structure]]		[[Category: Unliganded structure]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

OCA at 07:56, 2 April 2014

OCA — Wed, 02 Apr 2014 07:56:14 GMT

←Older revision		Revision as of 07:56, 2 April 2014
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].	+	[[3tgq]] is a 4 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=3TGQ OCA].

	==See Also==		==See Also==
Line 10:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022451932</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022451932</ref><references group="xtra"/><references/>
-	[[Category: Human ~~immunodeficiency virus 1~~]]	+	[[Category: Human]]
	[[Category: Kwon, Y D.]]		[[Category: Kwon, Y D.]]
	[[Category: Kwong, P D.]]		[[Category: Kwong, P D.]]

OCA at 11:07, 11 March 2013

OCA — Mon, 11 Mar 2013 11:07:39 GMT

←Older revision		Revision as of 11:07, 11 March 2013
Line 1:		Line 1:
-	[[Image:3tgq.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3tgq", 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_3tgq\| PDB=3tgq \| SCENE= }}		{{STRUCTURE_3tgq\| PDB=3tgq \| SCENE= }}
-
	===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===		===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22451932}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22451932 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_22451932}}		{{ABSTRACT_PUBMED_22451932}}

	==About this Structure==		==About this Structure==
	[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].		[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].
		+
		+	==See Also==
		+	*[[Gp120\|Gp120]]

	==Reference==		==Reference==

OCA at 05:19, 23 May 2012

OCA — Wed, 23 May 2012 05:19:57 GMT

←Older revision		Revision as of 05:19, 23 May 2012
Line 1:		Line 1:
-	[[Image:3tgq.~~jpg~~\|left\|200px]]	+	[[Image:3tgq.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===		===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22451932}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22451932 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22451932}}

	==About this Structure==		==About this Structure==
	[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].		[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022451932</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Kwon, Y D.]]		[[Category: Kwon, Y D.]]

OCA at 06:14, 4 April 2012

OCA — Wed, 04 Apr 2012 06:14:31 GMT

←Older revision		Revision as of 06:14, 4 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tgq.jpg\|left\|200px]]

-	The ~~entry 3tgq~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tgq", 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_3tgq\| PDB=3tgq \| SCENE= }}

-	~~Authors: Kwon,Y.D., Kwong, P.D.~~	+	===Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core===

-	~~Description: Cyrstal~~ structure ~~of unliganded HIV~~-1 ~~YU2~~ gp120 ~~core~~	+
		+	==About this Structure==
		+	[[3tgq]] is a 4 chain structure with sequence from [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=3TGQ OCA].
		+	[[Category: Human immunodeficiency virus 1]]
		+	[[Category: Kwon, Y D.]]
		+	[[Category: Kwong, P D.]]
		+	[[Category: Hiv-1 gp120]]
		+	[[Category: Unliganded structure]]
		+	[[Category: Viral protein]]

OCA at 07:31, 7 December 2011

OCA — Wed, 07 Dec 2011 07:31:17 GMT

←Older revision		Revision as of 07:31, 7 December 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tgq is ON HOLD	+	The entry 3tgq is ON HOLD until Paper Publication

	Authors: Kwon,Y.D., Kwong, P.D.		Authors: Kwon,Y.D., Kwong, P.D.

	Description: Cyrstal structure of unliganded HIV-1 YU2 gp120 core		Description: Cyrstal structure of unliganded HIV-1 YU2 gp120 core

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

OCA — Wed, 24 Aug 2011 07:13:21 GMT

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

←Older revision

Revision as of 07:13, 24 August 2011