Fig. 2: A partially open intermediate on the HIV-1 entry pathway retains FP accessibility to antibody binding.
From: Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening
A Three views of Population 1 structure shown in cartoon representation with gp41 colored black, gp120 gray, CD4 yellow, VRC34.01 blue, 17b orange. Glycans are shown as sticks. FP within the gp41 subunit is colored cyan. Within gp120, bridging sheet is colored red and α0 helix green. B Population 1 coordinates including Env (gp120 in gray, gp41 in black) and CD4 (yellow) fitted into the in situ cryo-ET reconstruction of a partially open CD4-bound Env (EMD-29294). C (Left to right) Vectors describing position of gp120 relative to gp41. The gp120 structure (blue), gp120 V1/V2 region (green), and gp41 (orange) in the closed state overlayed with the centroid locations depicting the dihedral, angles, and distances describing the position of gp120 relative to gp41. Dihedral, angle, and distance values for closed, intermediate, and open state structures. Data shown as scatter dot plots with horizontal lines indicating the mean and standard deviation. List of structures used for the calculations is provided in Supplementary Table 3. Source data are provided as a Source Data file. D (Left) Population 1 protomer shown in surface representation zoomed-in at the location of the FP. FP is shown in cartoon representation. The gp120 subunit is colored light gray, gp41 black, FP cyan and FPPR pale green. (Middle) One protomer of the partially open Env bound to CD4, 17b Fab and 8ANC195 Fab (PDB ID: 6CM3) shown in surface representation zoomed-in at the location of the FP (shown in cartoon representation). The gp120 subunit is colored gray, gp41 black, FP dark teal and FPPR light pink. (Right) Overlay of a Population 1 protomer with a protomer of a partially open CD4,17b,8ANC195-bound Env (PDB ID: 6CM3). The gp120 subunits were used for the superposition. Inset zooms in on the FP and FPPR. Zoomed-in panel is slightly rotated compared to zoomed-out view for better visualization. The solid lines (pale green for Population 1 and light pink for 6CM3) show the distance between FPPR residues Gln 540 and gp120 residue Phe 223.
