Figure 5

Docking of coordinates into gp140 and gp140-CD4m density maps and location of epitopes and 2D segmentation of unbound gp140 map.

(A) Side view of gp140 structure with SIV unliganded gp120 X-ray coordinates (PDB: 2BF1) docked. V1/V2 stem is in magenta, CD4 binding site is red and V4 loop is green. Arrows point to potential N-linked glycosylation sites on V4 near the trimer apex. Solid surface represents predominant density, with weaker density shown in mesh. Scale bar = 50 Å. Dashed rectangle outlines detail shown in (C). (B) Likely binding orientation of CD4 (yellow) to gp140. Note the restricted accessibility to the CD4BS conferred by density near the threefold, attributed to heavy glycosylation in the V4 region. Arrows are shown in same orientation as in (A). (C) Juxtaposition of the truncated V1/V2 loop stem with the bifurcated density proximal to the viral membrane confirms our earlier V2 location. Arrow points to V1/V2 stem, as V1/V2 was truncated from the coordinates. (D) 2D segmentation of unbound gp140 map at low gradient magnitudes (mesh) and high gradient magnitudes (solid), from a top view, reveals that the variable loop regions at the base of the trimer disappear when map is visualized at high gradient intensities, suggesting that these regions are structurally malleable and not rigid. Core of the protein at the center is evident at high gradient magnitudes, suggesting that there is little change in voxel intensity rate of change defining the core of the structure, as opposed to the variable loops. At right, the proximity of the basal V2 (red) and apical V3 (green) promote intersubunit contacts, decreasing trimeric diameter in the unliganded state. (E) Model of quaternary effects of V2 deletion and CD4m binding. At left, the full length trimer shows a robust gp120-gp41 interface and interprotomer interactions between V2 and V3′ loops. The gp120-gp41 interface is partly diminished following V2 deletion, while interprotomer contacts are abrogated, resulting in a relaxed trimer with a larger diameter. Binding of CD4/CD4m results in further weakening of the gp120-gp41 interface, subunit rotation (as exemplified by the rotated CD4BS) and enhanced exposure of the V3 loop.