Fig. 4
Inherent flexibility and effect of the binding of antibodies on trimer opening. a Inter-domain flexibility observed by aligning the trimeric gp120 and gp41 individually on the Env spike for available HIV trimer structures, in contrast to the overall Cα RMSDs (Å) of the trimeric gp140s also illustrated on the right. b Contribution of HR2 to the movement observed at the base of the HIV Env constructs measured in Cα RMSD (Å) as in a. Rotation (°) between the gp120/gp41 domains measured on the soluble Env with respect to BG505 NFL.664. To calculate subdomain rotation, the angle between gp120/gp41 was measured using three points on the Env, namely, Cα atoms of the conserved W571 and Q591 on HR2 and a pseudoatom placed at the center of mass (https://pymolwiki.org/index.php/Center_of_mass) of gp120. This value was then subtracted from the angle measured for BG505 NFL.664 to infer rotation between the subdomains. c A list of the available Env trimer structures with a description of the epitope(s) occupied, resolution (Å), space group, Env component in the asymmetric unit (ASU), and the distances between E654 on each protomer marking the coordinates at the Env base as sides of the triangle a, b and c. d Inter-V2 distances (Å) measured between R166 (Cα) on each gp41 at the trimer apex for available HIV trimer structures of various isolates and designs in c
