2NY1 image
Deposition Date 2006-11-20
Release Date 2007-02-06
Last Version Date 2024-10-30
Entry Detail
PDB ID:
2NY1
Title:
HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4 and Antibody 17b
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.99 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ENVELOPE GLYCOPROTEIN GP120
Gene (Uniprot):env
Mutations:I109C, T257S, S334A, S375W, Q428C
Chain IDs:A
Chain Length:317
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:T-cell surface glycoprotein CD4
Gene (Uniprot):CD4
Chain IDs:B
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:ANTIBODY 17B, LIGHT CHAIN
Gene (Uniprot):IGK@
Chain IDs:C
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:ANTIBODY 17B, HEAVY CHAIN
Gene (Uniprot):DKFZp686I15212
Chain IDs:D
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Ligand Molecules
Peptide-like Molecules
PRD_900003
Primary Citation
Structural definition of a conserved neutralization epitope on HIV-1 gp120.
Nature 445 732 737 (2007)
PMID: 17301785 DOI: 10.1038/nature05580

Abstact

The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.

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Primary Citation of related structures