Fig. 4: Structural basis for broad CoV recognition by CV3-25.

a Structural alignment of stem helix peptides to CV3-25 Fab and B6 Fab (PDBid: 7M53) shown as ribbon diagram. B6 heavy chain is shown in dark blue and light chain in light blue. CV3-25 heavy chain is shown in green and light chain in cyan. The B6-bound peptide is shown in yellow and the CV3-25-bound peptide in orange. b Left, structural alignment of the CV3-25 structure and the stem helix structure (PDBid: 6XR8) shown in cartoon representation. The 6XR8 stem helix is shown in dark gray and the CV3-25-bound peptide is shown in orange. Asn₁₁₅₈ glycan is shown in yellow sphere representation. Left, the alignment with a single protomer, right, an alignment with the trimer with the location of the glycan clash marked by a red X. c Structural alignment of CV3-25 to MD simulation model of the stem helix and HR2 region of the spike protein⁷⁰. Asp₁₁₅₈ glycan is shown in yellow sphere representation. Left, an alignment with a single protomer, right an alignment with the trimer. d Potential interaction area of the N-terminal end of HR2 and the light chain of CV3-25 is shown in tan. e Sequence alignment of the stem helix region of several CoV spike proteins. The peptide bound to CV3-25 is marked by the orange bar and crucial interacting residues are marked by *. The residues conserved in the binding site are shown in red. The region that could interact with the light chain is shown with the tan bar and the conserved region is highlighted by the blue box with similar residues shown in teal. f Structural alignment of the CV3-25 bound peptide (orange) to the post-fusion S (black, PDBid: 6XRA). The peptide was aligned to ₁₁₅₂LDKY₁₁₅₅ in the spike. Left, the alignment to the protomer. The sidechains of the residues are shown in stick representation, right, the region is shown in context of the trimer.