Fig. 4.

Segmentation of gp140 reveals density gap colocalizing with inner-outer domain boundary. (A) Volume rendering of unliganded gp140 docked with unliganded SIV gp120 in an oblique view with segmentation slice reveals areas of higher density (in red) compared to areas of lower density (in yellow, green, and blue). A clear separation between high density domains is observed while slicing through volume, which is likely indicative of the boundary between inner and outer domains. Arrow is pointing at the likely orientation of CD4 as it binds to the CD4-binding residues. (B) Volume rendering of CD4m-bound gp140 in an oblique view with segmentation slice reveals a uniform area of high density. As opposed to native, unliganded gp140, no discernable gap in high density areas is seen, suggesting closer association between the inner and outer domains of gp120. Arrow points to the location of the CD4 binding site subsequent to rotation of gp120 as described in Fig. 2. (C) Coordinates of unliganded SIV gp120 with slice from unliganded gp140 density map. Tilt reveals localization of the density gap at the inner-outer domain interface. (D) Coordinates of CD4-bound HIV-1 gp120 with slice from CD4m-bound gp140 density map. Tilt reveals lack of density separation, with corresponding closer association between inner and outer domains as observed in the coordinates.