Fig. 6: Cryo-EM structure of HmAb64 in complex with a tier-2 HIV-1 CNE40 Env trimer.

a Cryo-EM density of HmAb64 in complex with CNE40 Env in two perpendicular views. The regions corresponding to gp120, gp41, and N-linked glycans, as well as heavy and light chains of bound HmAb64, were colored light gray, dark gray, green, blue, and light blue, respectively. b Refined cryo-EM structure of HmAb64 in complex with CNE40 Env with the same color usage as in (a) and the CD4-binding loop of gp120 highlighted in orange. c Surface representation of the HmAb64-bound Env trimer with HmAb64 epitope colored blue and the footprint of CD4 outlined in purple. d Comparison of the HmAb64-bound open form Env trimer (blue) with the closed form (gray) and the open occluded form trimer recognized by b12 (teal). Each gp120 and gp41 subunit was represented by two conserved helices, α1/α2, and HR1/HR2, respectively, in cylinders (also see Supplementary Fig. 8). e Superimposition of sCD4 (purple) onto an HmAb64-bound gp120 in the same orientation as boxed in (a). The signature residue of CD4, Phe43, was highlighted in the sticks to indicate the approximate position of the Phe43 cavity. f Key residues in the CD4-binding loop and HmAb64 at the interface between gp120 and HmAb64. g Mapping of HmAb64 epitope on CNE40 gp120. Epitope residues were highlighted in gray shade, with those forming hydrogen bonds colored red and those forming salt bridges underlined. Amino acids that were disordered in the cryo-EM structure were shown in light gray font. Secondary structures of the antibody-binding regions were shown for reference. h Mapping of HmAb64 paratope. Paratope residues were highlighted in the gray shade, with those forming hydrogen bonds colored red and those forming salt bridges underlined. Only two SHM residues were involved in direct contact with gp120. The sequences were numbered according to the Kabat nomenclature.