Extended Data Fig. 5: Structures and epitopes of Fab:RBD complexes.

a, Surfaces targeted by broadly binding RBD antibodies. RBD surface is coloured by site variability across sarbecoviruses. ACE2 key motifs shown in transparent red cartoon. Antibody variable domains shown as cartoon, with darker shade indicating the heavy chain. b, c, Integrative features of the S309 (b) and S2X35 (c) structural epitopes. Details as in Figs. 3g, h, 2b. Variants in the S309 epitope were tested with VIR-7831 with the exception of E340D (marked with *), which was tested with S309. d–h, Zoomed in view of the RBD bound to S309 (d), S2X35 (e), S2H97 (f), S2E12 (g), and S2D106 (h), with important contact and escape residues labelled. RBD residues coloured by total site escape [scale bar, right of (d)]. i, j, Representative electron micrograph and 2D class averages of SARS-CoV-2 S in complex with the S2H97 Fab embedded in vitreous ice. Scale bar: 400 Å. Micrographs representative of 3138 micrographs. k, Gold-standard Fourier shell correlation curve for the S2H97-bound SARS-CoV-2 S trimer reconstruction. The 0.143 cut-off is indicated by a horizontal dashed line. l, Local resolution map calculated using cryoSPARC for the whole reconstruction with two orthogonal orientations. m, n, Representative electron micrograph and 2D class averages of SARS-CoV-2 S in complex with the S2D106 Fab embedded in vitreous ice. Scale bar: 400 Å. Micrographs representative of 2166 micrographs o, Gold-standard Fourier shell correlation curves for the S2D106-bound SARS-CoV-2 S trimer (black line) and locally refined RBD/S2D106 variable domains (grey line). The 0.143 cut-off is indicated by a horizontal dashed line. p, Local resolution map calculated using cryoSPARC for the whole reconstruction and the locally refined RBD/S2D106 variable ___domain region.