Extended Data Fig. 2: Cryo-EM analysis of SIVE660.CR54 SOS-2P in complex with ITS92.02 reveals a trimer with high flexibility at the apex.

a, Representative micrograph and CTF of the micrograph are shown. 8,259 micrographs were collected in total. b, Representative 2D class averages are shown. c, The gold-standard Fourier shell correlation resulted in a resolution of 4.32 Å using non-uniform refinement with C3 symmetry. d, The orientations of all particles used in the final refinement are shown as a heatmap. e, The local resolution of the full map is shown generated through cryoSPARC using an FSC cutoff of 0.5. f, A wild-type sequence alignment near the ITS92.02 epitope is shown highlighting residues within a 5 Å footprint in red. We note that non-conserved residue E613 forms a salt bridge with R94 of the ITS92.02 heavy chain. g, The prefusion (magenta) and postfusion (gray, PDB ID 1QBZ) conformations of gp41 protomers are aligned with the prefusion footprint residues colored red and the corresponding residues in the postfusion conformation are shown in blue. Footprint residues between positions 638 and 652 (HXB2 numbering) align well, residues from 608–614 extend away from the helical region of the epitope.