Fig. 4: Crystal structures of 3D1 complexed with cognate peptides from SARS-CoV-2 and HCoV-229E.

Overall view of the 3D1-pep^DVVNQN (a) and 3D1-pep^DVVNQQ (b) complex structures. The heavy and light chains of 3D1 are shown as cyan and orange semi-transparent surfaces, respectively, with all six CDRs depicted as cartoons. The 3D1-bound peptides are shown in green and presented in cartoon and stick representations, with the main chain hidden. The underlying CDR loops are also depicted in cartoon representation. Refined 2Fo−Fc electron density maps of the peptides (contoured at 1σ and within 2 Å of selected atoms) are located between residues D950 and N955 of HR1^SC2 (c) and residues D835 and Q840 of HR1^229E (d), bound to 3D1. The peptides are shown in stick representation (green carbon). The N-terminus and C-terminus of each peptide are indicated (Nterm/Cterm). Interfaces between the heavy and light chains with pep^DVVNQN (e) and pep^DVVNQQ (f) are also shown. Type I β-turns are highlighted with transparent grey circles for peptides from HR1^SC2 (g) and HR1^229E (h) bound to 3D1. Intrapeptide hydrogen bonds that emulate a pseudo 310 turn between the side chain of the first Asn and the amide backbone of the third residue in the turn are shown as black dashed lines. Ramachandran plots for the dihedral angles of 3D1-bound pep^DVVNQN (g, right panel) and pep^DVVNQQ (h, right panel) are provided. Residues with dihedral angles indicative of canonical type I β-turns are colored green; otherwise, they are colored blue.