Structure of a Natively-glycosylated HIV-1 Env Reveals a New Mode for VH1-2 Antibody Recognition of the CD4 Binding Site Relevant to Vaccine Design

Background: Structural studies of broadly neutralizing antibodies (bNAbs) bound to Env trimers have revealed mechanisms by which bNAbs targeting various epitopes penetrate the glycan shield to either accommodate or include N-glycans in their epitopes. Although accessibility to the conserved host receptor (CD4) binding site (CD4bs) is restricted by surrounding glycans, VRC01-class bNAbs mimic CD4 binding to share a common mode of gp120 binding and glycan accommodation using a VH1-2*02- derived variable heavy (VH) domain. While attractive candidates for immunogen design, features of VRC01-class bNAbs such as a high degree of somatic hypermutation (SHM) and a short (5-residue) light chain (LC) complementarity determining region 3 (CDRL3) (found in only 1% of human LCs) suggest they might be difficult to elicit through vaccination. However, we recently isolated a VH1-2*02-derived CD4bs bNAb, named IOMA, that includes a normal-length (8 residues) CDRL3. Methods: We used X-ray crystallography to solve the first structure of a fully- and natively-glycosylated Env trimer in complex with IOMA, and the V3-loop-directed bNAb 10-1074. Results: Our structure revealed antibody-vulnerable glycan holes and roles of complex-type N-glycans on Env that are relevant to vaccine design, while also demonstrating that IOMA is a new class of CD4-mimetic bNAb that contains features of both VH1-2/VRC01-class and VH1-46/8ANC131-class bNAbs. Conclusions: Analysis of the native glycan shield on HIV-1 Env allows the first full description of the interplay between heterogeneous untrimmed high-mannose and complex-type N-glycans within the CD4bs, V3-loop, and other epitopes on Env. In addition, the structural characterization of IOMA revealed an alternative pathway from VRC01-class bNAbs relevant to vaccine design, which could more readily lead to an effective vaccine response due to higher frequencies of normal-length CDRL3s compared with the rare 5-residue CDRL3s required for VRC01-class bNAbs, and a lower need for SHMs