Crystal Structure of PG16 and Chimeric Dissection with Somatically Related PG9: Structure-Function Analysis of Two Quaternary-Specific Antibodies That Effectively Neutralize HIV-1

HIV-1 resists neutralization by most antibodies. Two somatically related human antibodies, PG9 and PG16, however, each neutralize 70 to 80% of circulating HIV-1 isolates. Here we present the structure of the antigen-binding fragment of PG16 in monoclinic and orthorhombic lattices at 2.4 and 4.0 Å, respectively, and use a combination of structural analysis, paratope dissection, and neutralization assessment to determine the functional relevance of three unusual PG9/PG16 features: N-linked glycosylation, extensive affinity maturation, and a heavy chain-third complementarity-determining region (CDR H3) that is one of the longest observed in human antibodies. Glycosylation extended off the side of the light chain variable domain and was not required for neutralization. The CDR H3 formed an axe-shaped subdomain, which comprised 42% of the CDR surface, with the axe head looming ∼20 Å above the other combining loops. Comprehensive sets of chimeric swaps between PG9 and PG16 of light chain, heavy chain, and CDR H3 were employed to decipher structure-function relationships. Chimeric swaps generally complemented functionally, with differences in PG9/PG16 neutralization related primarily to residue differences in CDR H3. Meanwhile, chimeric reversions to genomic V genes showed isolate-dependent effects, with affinity maturation playing a significant role in augmenting neutralization breadth (P = 0.036) and potency (P < 0.0001). The structural and functional details of extraordinary CDR H3 and extensive affinity maturation provide insights into the neutralization mechanism of and the elicitation pathway for broadly neutralizing antibodies like PG9 and PG16.To create antibodies capable of effectively neutralizing human immunodeficiency virus type 1 (HIV-1), the adaptive humoral response is driven to exceptional lengths (reviewed in reference 8). Indeed, the response often fails, and sera from individuals infected with HIV-1 typically display limited neutralization breadth (59). After several years of infection, however, antibodies capable of neutralizing diverse viral strains develop in 15 to 25% of infected individuals (3, 16, 32, 33, 49, 53). Details of the adaptive changes that allow for effective recognition are of direct vaccine relevance, and clues from rare neutralizing antibodies have been eagerly sought.Two broadly neutralizing antibodies, PG9 and PG16, were recently identified with single cell-sequencing techniques after direct microneutralization assessment of secreted antibody from individually plated, stimulated B cells (58). These antibodies are somatically related and appear to be derived from the same recombination of heavy and light chains. They both recognize a site on HIV-1 gp120 composed of elements from the second and third variable regions (V2 and V3). Despite the vaunted diversity of the HIV-1 gp120 envelope and the even higher sequence variability in the V2 and V3 regions (26), neutralization assays indicate that the recognized epitope is conserved in 70 to 80% of circulating viral isolates (58).To investigate the molecular features of PG9 and PG16 that account for their neutralization effectiveness, we prepared antigen-binding fragments (Fabs) of each antibody and screened for crystallization. We were able to obtain a number of crystals, and those of PG16 proved suitable for structural analysis. Determination of the PG16 structure visualized several unusual features, and structure-function analysis indicated that two features, extensive affinity maturation and an exceptionally long heavy chain-third complementarity-determining region (CDR H3), were critical to its neutralization effectiveness. Barriers to eliciting these two features provide a likely explanation for the rarity of antibodies like PG9 and PG16; understanding and overcoming such barriers may form the basis for an effective HIV-1 vaccine.