Extended Data Figure 1: X-ray structure and epitope mapping of VH3–53 hNAb C102.
a, X-ray structure of C102 Fab – RBD331–518 complex. b, C102 CDR loops mapped on the RBD surface. b, Surface representation of C102 epitope colored by C102 HC (dark green) and LC (light green) interactions. c, CDRH1, CDRH2 and d, CDRH3 interactions with RBD residues. Potential H-bond contacts are illustrated as dashed lines. f, Left: Overlay of C102-RBD crystal structure (cartoon) with C105-S trimer cryoEM density (PDB 6XCM, EMD-22127) illustrating conserved binding to RBD epitope in an “up” conformation. Right: The C102 epitope is sterically occluded when aligned to a “down” RBD conformation (red and yellow star). SARS-CoV-2 S domains are dark gray (S2 domain) and light gray (S1 domain); the C105 Fab is yellow-green. g, Alignment of selected CDRH3 sequences for VH3–53/VH3–66 SARS-CoV-2 neutralizing antibodies (IMGT definition15). h, Overlay of hNAb COVA2–39 Fab4 (lime green and lemon, from COVA2–39-RBD structure, PDB 7JMP) and C144 Fab (blue, from C144-S structure) aligned on a RBDA of C144 epitope. COVA2–39 adopts a distinct conformation relative to the C102-like VH3–53/short CDRH3 NAb class and to C144, recognizing its RBD epitope only in an “up” RBD conformations due to steric clashes (red and yellow star) with the N343RBD-associated glycan on the adjacent RBD. i, Polyreactivity assay. IgGs were evaluated for binding to baculovirus extracts to assess non-specific binding. Polyreactive positive control IgGs were NIH45–46, NIH45–46G54W, and 45–46m2. Negative controls were bovine serum albuminn (BSA) and IgGs N6 and 3BNC117. Relative Light Unit (RLU) values are presented as the mean and standard deviation of triplicate measurements.