Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

Abstract

HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46–derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs.

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop

“…1 A and B). The BG505 Env in this complex adopts a conformation that is more open than the closed conformation in crystal and EM structures of Env trimers (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19), but less open than the conformation in low-resolution sCD4-bound Env structures (4-7) (Figs. 2 A and B and 3A) and an ∼9-Å cryo-EM reconstruction of the KN1144 SOSIP.681 soluble trimer bound to 17b in the absence of sCD4 (7).…”

“…Resolution limitations in the Env-sCD4-17b-8ANC complex structure precluded ab initio building of V1V2 residues into EM density. However, we could use available V1V2 coordinates to interpret the density because evidence suggests that the V1V2 loop is likely to maintain its overall four-stranded Greek key β-sheet folding topology because this fold is preserved in closed Env trimer structures (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19) and in structures of V1V2-alone scaffolds (32,33) (Fig. 4A).…”

“…The coordinates of 8ANC195 [Protein Data Bank (PDB) ID code 4P9M] (23), 17b, and sCD4 (PDB 1RZJ) (30) were first docked into their corresponding densities, after which the gp41 coordinates from a BG505 trimer structure (PDB ID code 5CEZ) (9) were fit into density. For fitting gp120 densities, we deleted the V1V2 and V3 coordinates from a closed BG505 trimer structure (PDB ID code 5T3X) (10) and then changed the β2-β3 strand topology to match a CD4-bound gp120 core structure (PDB 1RZJ) (30). These gp120 coordinates were fit individually into protomer densities.…”

“…6) do not appear to prevent transition to the open state. Despite the plethora of recent crystal and EM structures at atomic and nearatomic resolutions of closed Env trimers, most in complex with broadly neutralizing antibodies (bNAbs) (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19), only low-resolution structures derived from cryo-electron tomography of HIV-1 virions have been available for sCD4-bound open Env trimers (4)(5)(6)(7).…”

“…Single-particle electron microscopy (EM) structures of recombinant native-like soluble Env gp140 trimers (SOSIPs) confirmed that they can adopt the same closed and open architectures as virion-bound Env trimers (5-7), thus the SOSIP substitutions (introduction of a disulfide bond linking gp120 to gp41 and an Ile→Pro mutation in gp41; ref. The closed conformation of HIV-1 Env is stabilized by interactions at the trimer apex mediated by the gp120 V1V2 loop (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). In the closed state, the V1V2 region shields the binding site for the coreceptor on the V3 loop (11, 16), but V1V2 interactions with V3 cannot be maintained when the gp120 protomers rotate and separate to create the CD4-bound open conformation.…”