Fig. 2: Comparison of Env protomer conformations.
a Molecular structures of the three protomers of the AD8 Env model were aligned using the gp120 subunits. The gp41 fusion peptide (FP), FPPR + HR1N, HR1C and α9 helix are colored violet, blue, red and orange, respectively. The inset shows that the α9 helices in the three protomers rotate through a range of 7.4°. b The molecular structures of the three protomers of the AE2.1 Env model, aligned and colored as in (a). The largest angle between two α9 helices is 11.7°. c The AD8 and AE2.1 Env trimer models were superimposed, based on alignment of one protomer (Chains C and D). In the superposed structures in the center, the AD8 Env model is colored gray and the AE2.1 model is colored according to the chain. The non-aligned protomers of the AE2.1 Env are closer to the trimer axis by 1.1 Å and 1.3 Å, relative to the corresponding AD8 Env protomers. Close-up side views of the density maps and models of an interprotomer interface with a larger opening angle (left) and a smaller opening angle (right) are shown, colored according to the chain. The HR1N region is shown in the close-up views. HR1N is an α-helix in the interprotomer interfaces with larger opening angles, whereas HR1N in the interface with a smaller opening angle is either poorly ordered (for AD8) or a loop (for AE2.1). d The AD8 and Env(–) trimer models were superposed, based on alignment of one protomer (Chains C and D). In the left panel, the AD8 Env is in gray and Env(–) in purple. The interprotomer interface with a small opening angle is indicated with a star; one of the interprotomer interfaces with a large opening angle is indicated with a circle. Close-up side views of the interprotomer interfaces with a smaller opening angle (star) and a larger opening angle (circle) are shown in the right panels. In the right panels, the Env(–) model is colored purple; the AD8 Env model is colored gray, except for specific highlighted regions, colored as in (a).
