Extended Data Fig. 7. Molecular dynamics flexible fitting (MDFF) suggests that the Env trimer bound to three CD4 molecules is in a partially open conformation.

a The time evolution of backbone-RMSD of 5VN3* comparing to the last frame of MDFF simulation with 6CM3. b–e Atomic models showing the positions of CD4 (b, d) and gp120 (c, e) before (grey) and after (coloured) MDFF simulation with 5VN3 (b, c) and 6CM3 (d, e). The colour gradient bar indicates the amount of movement between the two structures. f, g The cross-correlation coefficient (CCC) curve between the density map and the trajectories of MDFF simulations (5VN3 in f and 6CM3 in g). h The map-model Fourier shell correlation (FSC) curve between the density map and the trajectories of MDFF simulations (5VN3 in red and 6CM3 in blue). The membranes in the maps were masked out for the analyses.