1YYM image
Deposition Date 2005-02-25
Release Date 2005-05-03
Last Version Date 2023-10-25
Entry Detail
PDB ID:
1YYM
Title:
crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.26
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)
Gene (Uniprot):env
Chain IDs:A (auth: G), E (auth: P)
Chain Length:313
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:antibody 17b heavy chain
Chain IDs:C (auth: H), G (auth: R)
Chain Length:229
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:antibody 17b light chain
Chain IDs:B (auth: L), F (auth: Q)
Chain Length:214
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:F23, scorpion-toxin mimic of CD4
Chain IDs:D (auth: M), H (auth: S)
Chain Length:27
Number of Molecules:2
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Primary Citation
Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth.
Structure 13 755 768 (2005)
PMID: 15893666 DOI: 10.1016/j.str.2005.03.006

Abstact

The binding surface on CD4 for the HIV-1 gp120 envelope glycoprotein has been transplanted previously onto a scorpion-toxin scaffold. Here, we use X-ray crystallography to characterize atomic-level details of gp120 with this transplant, CD4M33. Despite known envelope flexibility, the conformation of gp120 induced by CD4M33 was so similar to that induced by CD4 that localized measures were required to distinguish ligand-induced differences from lattice variation. To investigate relationships between structure, function, and mimicry, an F23 analog of CD4M33 was devised. Structural and thermodynamic analyses showed F23 to be a better molecular mimic of CD4 than CD4M33. F23 also showed increased neutralization breadth, against diverse isolates of HIV-1, HIV-2, and SIVcpz. Our results lend insight into the stability of the CD4 bound conformation of gp120, define measures that quantify molecular mimicry as a function of evolutionary distance, and suggest how such evaluations might be useful in developing mimetic antagonists with increased neutralization breadth.

Legend

Protein

Chemical

Disease

Primary Citation of related structures