3IDY: Crystal Structure Of Hiv-Gp120 Core In Complex With Cd4-Binding Site Antibody B13, Space Group C2221

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.
PDB ID: 3IDYDownload
MMDB ID: 78182
PDB Deposition Date: 2009/7/22
Updated in MMDB: 2009/12
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Human immunodeficiency virus 1
Similar Structures:
Biological Unit for 3IDY: hexameric; determined by author
Molecular Components in 3IDY
Label Count Molecule
Proteins (6 molecules)
Hiv-1 Hxbc2 Gp120 Core
Molecule annotation
FAB B13 Heavy Chain
Molecule annotation
FAB B13 Light Chain
Molecule annotation
Chemicals (29 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB