Structural Superimposition

Abstact

The HIV-1 Envelope (Env) in its pre-receptor "closed" conformation is targeted by broadly neutralizing antibodies (bnAbs), while its receptor-bound "open" conformation exposes immunodominant epitopes targeted by non-neutralizing antibodies. A human immunoglobulin G (IgG) monoclonal antibody (mAb), 19b, binds an Env third variable (V3) loop epitope that is only exposed in the open Env conformation. Despite widespread use of 19b to detect the open Env conformation in immunoassays, its epitope has not yet been structurally defined. Here, we determine crystal structures of ligand-free and V3 peptide-bound 19b Fab to visualize details of this interaction. 19b utilizes both its heavy and light chains to interact with the V3 loop. The 5-residue heavy-chain complementarity-determining region (CDR H3) forms a hydrophobic binding pocket to bind V3 residues. 19b adopts a cradle-binding mode, with its CDRH1, CDRL2, and CDRL3 mediating interactions with the V3 regions flanking the conserved GPGR/Q motif, while making only limited contacts with the GPGR arch region. Our high-resolution structures elucidate the epitope, binding mode, and the structural basis for the broad reactivity of 19b, thereby filling a gap in our knowledge of a widely used reagent in immunoassays. IMPORTANCE: Here, we determine high-resolution crystal structures of 19b, an antibody that binds the receptor-bound "open" conformation of the HIV-1 envelope (Env) protein at an epitope located within its third variable (V3) loop. Despite widespread use of 19b to detect the open Env conformation in immunoassays, its epitope has not yet been structurally defined. Our high-resolution structures, by elucidating the epitope, binding mode and the structural basis for the broad reactivity of 19b, fill a gap in our knowledge of a reagent that is widely used in immunoassays.