Fig. 2. SARS-CoV-2 FP recognition by fp.006.
(A) Overview of the complex structure of fp.006 Fab (surface representation; heavy chain in teal, light chain in light teal) bound to the SARS-CoV-2 FP (orange cartoon) with interacting side chains represented as sticks. (B) Visualization of FP residues F823, E819, and R815 resting in a deep groove formed at the antibody paratope, with coloring as in (A). (C) Overlay of the fp.006-FP crystal structure with a cryo-EM structure of the SARS-CoV-2 prefusion S trimer (PDB: 6VXX). Models were aligned on Cα atoms of FP residues 818–822 (helical in both structures) with a root mean square deviation of 0.97 Å. (D) Residue-level interactions between FP residue R815 and the antibody heavy chain include hydrogen bond formation with N31 and a cation-π interaction with Y52A. (E) Water-mediated interactions between FP residue E819 and heavy chain residues Y52A, N56, and F97. Water molecules are shown as red spheres. (F) van der Waals contacts between FP residue F823 (orange stick) and residues that comprise a groove at the heavy and light chain interface (teal surfaces). (G) Interactions between FP residue D820 and fp.006 CDRH2 residues include a salt bridge with R55 and additional hydrogen bond formation with N56. Hydrogen bonds, salt bridges, and cation-π interactions are shown as dashed blue lines. (H) Flow cytometry detection of anti-FP and anti-HR2 antibody binding to SARS-CoV-2 S expressed on 293 T cells. Left, representative FACS plots (pre-gated on live-singlets-GFP+ cells). Black lines indicate isotype control in the presence (continuous line) or absence (dotted line) of soluble ACE2. Right, quantification of the geometric mean fluorescent intensity (gMFI; n = 3). Two-tailed paired t-test: *p < 0.05, **p < 0.01, ***p < 0.001 and ****p < 0.0001; standard deviation is shown.