Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization

Abstract

F425-B4e8 (B4e8) is a monoclonal antibody isolated from a human immunodeficiency virus type 1 (HIV-1)-infected individual that recognizes the V3 variable loop on the gp120 subunit of the viral envelope spike. B4e8 neutralizes a subset of HIV-1 primary isolates from subtypes B, C and D, which places this antibody among the very few human anti-V3 antibodies with notable cross-neutralizing activity. Here, the crystal structure of the B4e8 Fab' fragment in complex with a 24-mer V3 peptide (RP142) at 2.8 A resolution is described. The complex structure reveals that the antibody recognizes a novel V3 loop conformation, featuring a five-residue alpha-turn around the conserved GPGRA apex of the beta-hairpin loop. In agreement with previous mutagenesis analyses, the Fab' interacts primarily with V3 through side-chain contacts with just two residues, Ile(P309) and Arg(P315), while the remaining contacts are to the main chain. The structure helps explain how B4e8 can tolerate a certain degree of sequence variation within V3 and, hence, is able to neutralize an appreciable number of different HIV-1 isolates.

Figure 1

Crystal structure of the B4e8-RP142 complex. The peptide is colored in yellow and the Fab’ heavy and light chains in dark and light gray, respectively; the Fab’ CDR loops are colored in orange for L1, purple for L2, red for L3, cyan for H1, salmon for H2 and light green for H3. The sugar and Asn^H28, to which it is linked, are shown in stick representation and colored in dark green. Images were produced with Pymol (http://pymol.sourceforge.net/).

Figure 2

New canonical class for CDR L3. (a) Comparison of the CDR L3 loop of B4e8 (red) to members of canonical class κ-1 (PDB-code: 1REI, lightblue), κ-2 (2FBJ, yellow), κ-3 (1YQV, aquamarine), κ-4 (1DFB, salmon) and κ-5 (palegreen, 1BAF). (b) The B4e8 kappa chain CDR L3 has an Asp instead of the usual Pro at position 95a and represents a new canonical structure.

Figure 3

Electron density (2F_obs-F_calc) for the RP142-peptide in complex with B4e8, contoured at 1.0σ. All residues, except the side chains of Lys^P305 and Arg^P304, are well defined.

Figure 4

Specific binding interactions between B4e8 and RP142. Atomic coloring is used for the atoms with the carbon atoms of the peptide colored in yellow, carbon atoms of the heavy chain in light blue and those of the light chain in pale green. Only those residues of the Fab’ that make contact to the peptide are shown in stick representation. Residues Gly^P312 - Ala^P316 form a five residue α-turn.

Figure 5

Detailed view of the exposed Arg^P315 and its interactions with B4e8. Hydrogen bonds and salt bridges are shown by dashed lines. Color coding is as in Fig. 4. Arg^P315 is sandwiched between Phe^P317 and Tyr^L32 and stabilized by a salt bridge and a hydrogen bond to the side chain and backbone of Asp^L92. The unusual α-turn conformation is stabilized by two hydrogen bonds between Asn^H100d and the backbone of Arg^P315 and Pro^P313, respectively.

Figure 6

Molecular surface representation of the antigen-binding pocket colored by electrostatic potential, calculated in APBS, and mapped onto the surface with the color code ranging from -10 kT/e (bright red) to +10 kT/e (dark blue). Ile^P309 is accommodated in a hydrophobic pocket, whereas Arg^P315 forms a salt bridge with Asp^L92.

Figure 7

Comparison of V3-peptides RP142 and MN bound to B4e8 (atomic coloring with carbon atoms in yellow) and 2219 (carbon atoms in light blue), respectively. Identical residues in both peptides are labeled only for B4e8 (black). Identical hydrogen bonds are marked by dashed lines and shown only for B4e8. Due to the conversion from a type II β-turn in 2219 to an α-turn in B4e8, one hydrogen bond in the apex of RP142 is lost in the complex with B4e8. The β-hairpin conformation is maintained by a one-residue shift accompanied by a 180° rotation of Ala^P316 and all subsequent residues. Residues P304 to P306 and P319 to 320 are omitted for clarity.