Fig. 2
Comparison of apo- and Env-bound BG18 variable domains. a Superposition of VH-VL domains (230 Cα atoms) of unliganded BG18 (deep teal; PDB 5UD9 (http://dx.doi.org10.2210/pdb5UD9/pdb)) with BG18 in the BG18-BG505 structure (blue) showed conservation of the BG18 antigen-binding site and ordering of CDRL2 in the BG505-bound structure (dashed red line represents disordered CDRL2 in unliganded BG18). b Surface representation of BG18 in the BG505-bound structure showed conservation of BG18 clefts, including the cleft between CDRH3 and CDRL1/3 loops observed in the BG18 apo structure47. c Ribbon and cartoon representation of the overlay between BG18 (aligned on the Fab VH domains) in the BG18-BG505-35O22 complex (blue), unliganded BG18 (deep teal), and unliganded 10-1074 (magenta; PDB 4FQ2 (http://dx.doi.org10.2210/pdb4FQ2/pdb)). CDRH3 loops for the three structures are represented as cartoons. Inset: overlay of BG18-BG505 and 10-1074-BG505 (PDB 5T3Z (http://dx.doi.org10.2210/pdb5T3Z/pdb)) CDRH3 loops. d Cartoon and stick representation of BG18 CDRH3 recognition of the N332gp120 glycan. BG18 residues comprising a conserved structural motif (R-I-Y-G-V/I-I) are labeled. Electron density contoured at 1σ from 2Fobs−Fcalc composite annealed omit map calculated with phases from models with the N332gp120 glycan and BG18 CDRH3 coordinates omitted to reduce potential phase bias (cyan and blue mesh)
