Fig. 5: Antigen recognition of 3D1.

a Crystal structures of apo 3D1 (left panel), 3D1-pep^DVVNQN (middle panel), and 3D1-pep^DVVNQQ (right panel) are shown as electrostatic potential surfaces. The quality of electron density at K54 of 3D1 (middle and right panels) is presented in a close-up view. Peptide epitopes are colored green and depicted in cartoon and stick representations, with the main chain hidden. b Overall view of interactions between 3D1 and pep^DVVNQN. Residues in the paratope and epitope are shown as sticks. Detailed interactions between 3D1 and HR1^SC2 are highlighted using black dashed lines. 3D1 is represented as a cartoon, with residues from pep^DVVNQN shown in either stick or cartoon format. The light chain is depicted in orange, while the heavy chain is depicted in cyan. Residues engaging in interactions are shown as sticks and labeled. Residues involved in side chain-to-main chain hydrophilic interactions are underlined. Peptide residues that mediate both side chain-to-side chain and side chain-to-main chain interactions are boxed. c, d Featured binding properties of Q954^SC2 with 3D1 mAb. The terminal acylamino group of the side chain of Q954^SC2 forms a pair of hydrogen bonds with N35^HFW2 (c), and Trp-Asn interactions are presented in (d). The center of the aromatic ring is indicated with red pseudo dots. e Sensorgram of 3D1 mutants binding to HR1C by BLI. The 3D1 mutants that significantly affect 3D1 mAb binding are shown in color, while the wild-type 3D1 is shown in black. f Alanine scan mutagenesis of the linear epitope of pep^DVVNQN. The binding constants between 3D1 and each mutant peptide were measured by BLI. NA indicates no binding detected. The bar graph displays interaction contributions between corresponding epitopic residues and heavy (cyan color) or light chain (orange color) of 3D1 caculated by PISA. g Neutralization of SARS-CoV-2 pseudovirus wild-type and mutant strains. The wild-type virus is shown in blue, while the mutant viruses are depicted in assorted colors. Results are presented as mean ± SD, derived from two replicate experiments.