Fig. 5: Binding mode and epitope specificity of five bnAbs to SARS-CoV-2.

a–e, Crystal or cryo-EM structures of five Fab fragments complexed with RBDs derived from wild-type, beta or omicron BA.1. All RBDs are colored in cyan whereas P5S-2B10 (a) is in red, P5-1H1 (b) is in green, P2S-2E9 (c) is in magenta, P5S-3B11 (d) is in orange and P2-1B1 (e) is in purple. f, Fab fragments of P5S-2B10, P5-1H1, P2S-2E9, P5S-3B11 and P2-1B1 complexed with RBDs superimposed into one composite together with receptor ACE2 (brown). g, The footprints of P5S-2B10, P5-1H1 and P2-1B1 Fabs, together with those of S2E12 and ACE2, shown on the surface of the SARS-CoV-2 RBD. The epitope residues are indicted just below each structure, with the mutation sites found in omicron BA.1 indicated in red. h, Comparison of the epitope residues of the P5S-2B10, P5-1H1, P2-1B1, P2S-2E9 and P5S-3B11 antibodies with published representative antibodies and the receptor ACE2 along the linear RBD sequence. A logo plot of RBD sequences was created based on all tested SARS-CoV-2 variants. The numbering system follows that in the GISAID database. i,j, The footprints of P2S-2E9 (i) and P5S-3B11 (j) Fabs, together with those of representative antibodies and ACE2, shown on the surface of the SARS-CoV-2 RBD. The epitope residues are indicted just below each structure, with the mutation sites found in omicron BA.1 indicated in red. The highly conserved N-glycosylation residue N343 among the sarbecoviruses is indicated.