4dkr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:56, 30 October 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:4dkr.png|left|200px]]
 
-
<!--
+
==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169==
-
The line below this paragraph, containing "STRUCTURE_4dkr", creates the "Structure Box" on the page.
+
<StructureSection load='4dkr' size='340' side='right'caption='[[4dkr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[4dkr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(BRU_ISOLATE) Human immunodeficiency virus type 1 (BRU ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DKR FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0LJ:N-[(1R,2R)-2-CARBAMIMIDAMIDO-2,3-DIHYDRO-1H-INDEN-1-YL]-N-(4-CHLORO-3-FLUOROPHENYL)ETHANEDIAMIDE'>0LJ</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-
{{STRUCTURE_4dkr| PDB=4dkr | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkr OCA], [https://pdbe.org/4dkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dkr RCSB], [https://www.ebi.ac.uk/pdbsum/4dkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkr ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q0ED31_9HIV1 Q0ED31_9HIV1] 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).[RuleBase:RU004292][SAAS:SAAS000328_004_020447] 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).
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Cellular infection by HIV-1 is initiated with a binding event between the viral envelope glycoprotein gp120 and the cellular receptor protein CD4. The CD4-gp120 interface is dominated by two hotspots: a hydrophobic gp120 cavity capped by Phe43(CD4) and an electrostatic interaction between residues Arg59(CD4) and Asp368(gp120). The CD4 mimetic small-molecule NBD-556 (1) binds within the gp120 cavity; however, 1 and related congeners demonstrate limited viral neutralization breadth. Herein, we report the design, synthesis, characterization, and X-ray structures of gp120 in complex with small molecules that simultaneously engage both binding hotspots. The compounds specifically inhibit viral infection of 42 tier 2 clades B and C viruses and are shown to be antagonists of entry into CD4-negative cells. Dual hotspot design thus provides both a means to enhance neutralization potency of HIV-1 entry inhibitors and a novel structural paradigm for inhibiting the CD4-gp120 protein-protein interaction.
-
===Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169===
+
Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.,Lalonde JM, Kwon YD, Jones DM, Sun AW, Courter JR, Soeta T, Kobayashi T, Princiotto AM, Wu X, Schon A, Freire E, Kwong PD, Mascola JR, Sodroski J, Madani N, Smith AB 3rd J Med Chem. 2012 Apr 23. PMID:22497421<ref>PMID:22497421</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 4dkr" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_22497421}}, adds the Publication Abstract to the page
+
*[[Gp120 3D structures|Gp120 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 22497421 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_22497421}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[4dkr]] is a 2 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=4DKR OCA].
+
[[Category: Courter JR]]
-
 
+
[[Category: Freire E]]
-
==Reference==
+
[[Category: Jones DM]]
-
<ref group="xtra">PMID:022497421</ref><references group="xtra"/>
+
[[Category: Kobayashi T]]
-
[[Category: Human immunodeficiency virus 1]]
+
[[Category: Kwon YD]]
-
[[Category: Courter, J R.]]
+
[[Category: Kwong PD]]
-
[[Category: Freire, E.]]
+
[[Category: LaLonde JM]]
-
[[Category: III, A B.Smith.]]
+
[[Category: Madani N]]
-
[[Category: Jones, D M.]]
+
[[Category: Mascola J]]
-
[[Category: Kobayashi, T.]]
+
[[Category: Princiotto AM]]
-
[[Category: Kwon, Y D.]]
+
[[Category: Schon A]]
-
[[Category: Kwong, P D.]]
+
[[Category: Smith III AB]]
-
[[Category: LaLonde, J M.]]
+
[[Category: Sodroski J]]
-
[[Category: Madani, N.]]
+
[[Category: Soeta T]]
-
[[Category: Mascola, J.]]
+
[[Category: Sun AW]]
-
[[Category: Princiotto, A M.]]
+
[[Category: Wu X]]
-
[[Category: Schon, A.]]
+
-
[[Category: Sodroski, J.]]
+
-
[[Category: Soeta, T.]]
+
-
[[Category: Sun, A W.]]
+
-
[[Category: Wu, X.]]
+
-
[[Category: Aws-i-169]]
+
-
[[Category: Cd4 mimic]]
+
-
[[Category: Clade a/e]]
+
-
[[Category: Hiv-1 gp120]]
+
-
[[Category: Viral protein-inhibitor complex]]
+

Current revision

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169

PDB ID 4dkr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4dkr"
Personal tools