Fig. 6: Cryo-EM structure of neutralizing antibodies 2130-1-0114-112 in complex with Omicron BA.2 RBD.

a, Atomic model of the RBD–Fab complex, coloured by chain: BA.2 RBD in red, 2130-1-0114-112 HC in yellow and 2130-1-0114-112 LC in green. BA.2 RBD mutations are in orange, and 2130-1-0114-112 mutations are in cyan and blue (HC and LC) (left). A close-up view of the RBD–Fab interface, showing WA1 RBD (Protein Data Bank 7L7E, light brown shading) aligned with the BA.2 RBD (right). b–d, Details showing the 2130-1-0114-112 modified residues and their interaction with BA.2 RBD, coloured as in a. Residue labels are shown in black for the BA.2 complex and brown for the overlaid WA1-2130 complex. The orange and green dashed lines indicate hydrogen bond and hydrophobic interactions, respectively; the yellow dashed lines are labelled with distances. CDRH3 residue Glu112 (left) and with the surface coloured by electrostatic potential (right), showing the positive and negative charges of RBD Lys444 and CDRH3 Glu112 (b). CDRL1 Ala32 and Ala33 hydrophobic network (left) and with the nearby RBD surface coloured by hydrophobicity (right; orange to cyan indicates hydrophobic to hydrophilic) (c). CDRL2 Glu59 salt bridge with RBD residue Arg498 (d). e, 2D diagram of Fab 2130-1-0114-112 paratope and epitope residues involved in hydrogen bonds and salt bridges (yellow and red dashed lines, respectively; distances in Å) and hydrophobic interactions (curved lines with rays). Atoms are shown as circles, with oxygen, carbon and nitrogen in red, black and blue, respectively. Interacting residues that belong to CDR loops are coloured in corresponding shades. The asterisks indicate mutated residues. Image created with Ligplot+³⁴.