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. 2016 Nov 15;113(46):E7151-E7158.
doi: 10.1073/pnas.1615939113. Epub 2016 Oct 31.

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

Haoqing Wang  1 , Alexander A Cohen  1 , Rachel P Galimidi  1 , Harry B Gristick  1 , Grant J Jensen  1   2 , Pamela J Bjorkman  3
Affiliations

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

Haoqing Wang et al. Proc Natl Acad Sci U S A. .

Abstract

The HIV-1 envelope (Env) glycoprotein, a trimer of gp120-gp41 heterodimers, relies on conformational flexibility to function in fusing the viral and host membranes. Fusion is achieved after gp120 binds to CD4, the HIV-1 receptor, and a coreceptor, capturing an open conformational state in which the fusion machinery on gp41 gains access to the target cell membrane. In the well-characterized closed Env conformation, the gp120 V1V2 loops interact at the apex of the Env trimer. Less is known about the structure of the open CD4-bound state, in which the V1V2 loops must rearrange and separate to allow access to the coreceptor binding site. We identified two anti-HIV-1 antibodies, the coreceptor mimicking antibody 17b and the gp120-gp41 interface-spanning antibody 8ANC195, that can be added as Fabs to a soluble native-like Env trimer to stabilize it in a CD4-bound conformation. Here, we present an 8.9-Å cryo-electron microscopy structure of a BG505 Env-sCD4-17b-8ANC195 complex, which reveals large structural rearrangements in gp120, but small changes in gp41, compared with closed Env structures. The gp120 protomers are rotated and separated in the CD4-bound structure, and the three V1V2 loops are displaced by ∼40 Å from their positions at the trimer apex in closed Env to the sides of the trimer in positions adjacent to, and interacting with, the three bound CD4s. These results are relevant to understanding CD4-induced conformational changes leading to coreceptor binding and fusion, and HIV-1 Env conformational dynamics, and describe a target structure relevant to drug design and vaccine efforts.

Keywords: CD4; HIV-1 Env trimer; HIV-1 coreceptor; conformational change; cryo-EM.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
An 8.9-Å EM reconstruction of Env–sCD4–17b–8ANC complex. (A and B) Electron density fit by coordinates for gp120 (gray), gp41 (orange), sCD4 D1 (yellow), 17b VH-VL (forest green), 17b CH-CL (chartreuse), 8ANC195 VH-VL (magenta), and 8ANC195 CH-CL (pink). N-linked glycan coordinates are shown as sticks. (A) Side view in which the threefold symmetry axis of the BG505 trimer is vertical. (B) Bottom view looking down the threefold symmetry axis of the BG505 trimer. (C) Side view of density of gp41 portion of the BG505 trimer. (D) Close-up of density near the N-linked glycan attached to BG505 Asn368gp120.
Fig. 2.
Fig. 2.
CD4-induced structural changes in Env trimers. (A) gp120 surface representations for the closed (PDB ID code 5T3X) (blue), partially open (this study) (gray), and sCD4-bound open Env structures (PDB ID code 3DNO) (green) as seen from the side. V1V2 loops (red) are depicted as surface representations for the closed and open structures and as EM density for the partially open structure. Locations of V3 (blue) and the CD4 binding site (CD4bs) (yellow) are depicted as surface representations. (B) gp41 in ribbon representation (closed and partially open Env structures) or as density (open Env structure) for Env structures. Because gp41 coordinates for an open Env structure were unavailable, we used the density from the single-particle EM structure of an open KNH1144–17b complex (EMDB entry 5462) (7). (C) Top view of gp120 representations shown in A. (D) Top view of gp41 representations shown in A.
Fig. 3.
Fig. 3.
Putative V1V2 densities. (A) Superposition of the gp140 (gp120 plus gp41) coordinates from one monomer in a closed BG505 Env trimer structure (PDB ID code 5T3X) (blue) and the gp140 coordinates from the 8.9 Å partially open BG505 Env trimer reported here (gray) as seen from two different orientations. The gp140 monomers were aligned by using the threefold symmetry axis of the gp41 trimer. The arrow in Left marks the axis about which a rotation of 30° and a translation of 2.6 Å relates the gp120 in the closed structure to the gp120 in the partially open structure. The V1V2 loop (red) is depicted as a ribbon for the closed trimer and as EM density for the partially open structure. The V3 loop (dark blue) is depicted as a ribbon for closed trimer and not shown in the partially open structure because it was disordered. The 8ANC195 Fab (magenta heavy chain; light pink light chain) is shown in Left based on its position with respect to the partially open gp140, illustrating that its epitope at the gp120–gp41 interface does not undergo extensive changes. (B) sCD4-proximal densities (red) in four independent CD4-bound Env structures: the 8.9-Å and 9.8-Å cryo-EM reconstructions of the Env–sCD4–17b–8ANC complex (this study), the 16.8-Å negative stain reconstruction of the Env–sCD4–17b–8ANC complex (18), and the ∼20-Å reconstruction of a sCD4-Env trimer structure derived from subtomogram averaging of virion-bound Env spikes (4). High contour level densities in the Env–sCD4–17b–8ANC reconstructions are shown in bright red and bright yellow for V1V2 and sCD4, respectively, with lower contour level densities in lighter colors.
Fig. 4.
Fig. 4.
V1V2 loop structures. (A) V1V2 folding topologies in V1V2 scaffold (PDB ID code 5ESV) (32, 33), closed BG505 trimer (PDB ID code 5FYJ) (10, 19), and molecular dynamics model of repositioned V1V2 in full-length CD4-bound gp120 (21). β-strand nomenclature in V1V2 is the same as in ref. . Disulfide bonds are shown as yellow sticks. (B–D) gp120s from structures of closed BG505 trimer (PDB ID code 5FYJ) (19) (B), sCD4-bound monomeric gp120 core (truncated V1V2 and V3 loops) (PDB ID code 1RZJ) (30) (C), and the molecular dynamics model of full-length CD4-bound gp120 (21) (D). Top shows structural overviews. Middle shows close-up views of the regions in the boxed areas. Bottom shows topology diagrams of the bridging sheet (adapted from ref. 16). V1V2 is red and V3 is blue. Strands β2 and β3, which precede and follow V1V2 in the gp120 sequence, are cyan and green, respectively. gp120 strands β20 and β21, which form a β-sheet with β2 and β3 in sCD4-bound gp120 structures (31) are orange and magenta, respectively.
Fig. 5.
Fig. 5.
V1V2 fitting to EM density. Densities are gray (gp120), orange (gp41), yellow (sCD4), and red (V1V2). (A) EM density map (high contour level) fit with coordinates of a sCD4-bound monomeric gp120 core (truncated V1V2 and V3 loops) (PDB ID code 1RZJ) (30). (B) Close-up of map and coordinates in A showing putative contacts between V1V2 loop stem and CD4 D1. (C) EM density map (low contour level for V1V2 and sCD4 regions) fit with coordinates of the molecular dynamics model of full-length CD4-bound gp120 (21). The V3 loop does not fit in the density. (D) Close-up of map and coordinates in C.
Fig. 6.
Fig. 6.
Interactions of 17b with BG505 and BG505-ΔV1V2. (A) SEC profile demonstrating that BG505-ΔV1V2, but not BG505, binds 17b Fab. (B) SDS/PAGE analysis of SEC fractions.
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