Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120

Abstract

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.

Fig. 1

Co-crystal structure of antibodies F105 and b13 in complex with HIV-1 gp120. (A) Fab F105 in complex with a YU2 gp120 core with intact V3. Polypeptide chains are depicted in ribbon representation, with F105 in dark and light blue for heavy and light chain, respectively, and gp120 in red (with β20/β21 and V1/V2 stem highlighted in green and cyan, respectively). (B) Cα-backbone traces for F105- and CD4-bound conformations of gp120. The F105-bound structure corresponds to the core with V3 determined here, whereas the YU2 structure corresponds to the original core, with V3 truncation (46). Dashed lines correspond to the disordered V3 (fig. S1) and V4 regions. (C) Similarities in recognition of Asp³⁶⁸ of gp120 by Arg^100F of F105 (blue) and Arg⁵⁹ of CD4 (yellow) (47). (D) Fab b13 in complex with an HXBc2 gp120 core restrained to be in the CD4-bound state. Polypeptide chains are depicted in ribbon representation with b13–heavy chain in purple, light chain in gray, and gp120 colored as in (A). (E) Cα-backbone traces for heavy chain of antibody b12 (green) and antibody b13 (purple) in complexes with gp120 (red) after gp120-outer domain superposition. (F) Heavy-chain complementarity-determining regions (CDRs) for b13 (purple) and b12 (green) binding the CD4-binding loop (red) of gp120.

Fig. 2

Epitopes, bound conformations, and trimer modeling. (A) Epitope hydrophobicity. The surface of gp120 is shown in gray, with hydrophobic residues highlighted in green. Binding surfaces for CD4, F105, b12, and b13 are outlined in orange. (B) Ligand-bound conformation of gp120. Polypeptides of gp120 are depicted in ribbon representation with inner domains shown in light gray, outer domains in dark gray, and regions that in the CD4-bound state correspond to the bridging sheet shown in red. Residues 109 and 428 are highlighted in blue and shown in stick representation. (C) Viral spike compatibility. Density maps derived from the cryo–electron tomography of HIV-1 BaL isolate spike are shown in gray for CD4 and 17b- and b12-bound states (first and third from left, respectively), along with optimal fits of atomic-level models (30). To model F105- and b13-bound forms of gp120 into likely viral spike orientations, the invariant β-sandwich of the gp120 inner domain was superimposed. Likely clashes of V1/V2 in the superimposed conformation with neighboring protomers close to the trimer axis are highlighted in light blue.

Fig. 3

Immune evasion at the site of initial CD4 attachment. (A) Recognition similarity. Centers of recognition for CD4, F105, b12, and b13. After superposition of gp120 outer domains, the centers of the recognition surface of each ligand on gp120 is denoted by balls for CD4 (yellow), F105 (blue), b12 (red), and b13 (purple). (B) Immune evasion. The initial site of CD4 attachment (cross-hatched yellow surface) is circumscribed by a combination of glycan (green) and conformational constraints. The surface on gp120 recognized by F105, b12, and b13 (that strays beyond the site of CD4 attachment) is shown in blue, red, and purple, respectively. Glycosylation sterically crowds the immune response toward the bridging-sheet region (blue surface that F105 recognizes) or toward the V3 region (purple surface that b13 recognizes) (48). In either case, recognition of these regions of gp120 results in antibody-bound conformations of gp120 that are poorly compatible with the functional spikes of HIV-1 virions from tier 2 primary isolates.