Fig. 5

Structures of NIEAs bound to the NTD protein of SARS-CoV-2 variants. (a) The epitopes of NIEAs, namely DH1052 (PDB: 7LAB), 8D2 (PDB: 7DZX), and COV2-2490 (PDB: 2DZY) face the viral membrane. NIEAs are shown as cartoon, and colored orange, light goldenrod yellow, and light cyan, respectively. The other parts are shown as surface. The related NTD of NIEAs is colored yellow. (b) Footprint of DH1052 on spike NTD. The light chain and heavy chain of DH1052 are colored orchid and blue. The footprint is colored cadet blue and circled out by violet red line. Sites that affect and those that do not affect antibody-mediated enhancement of infection are colored red and green, respectively. (c) Mutation sites of 12 different SARS-CoV-2 variants are mapped onto the NTDs. The accession numbers for the NTD atomic model in PDB are 7R14 (Alpha), 7R16 (Beta), 7VXC (Kappa), 8HRI (Delta), 7YBJ (Mu), 7YBM (C.1.2), 8HHZ (BA.1), 7XIW (BA.2), 7YQT (BA.2.75), 8IOS (XBB.1), 8XMT (EG.5.1) and 8XLV (BA.2.86). The key amino acids are shown as sticks. Mutated amino acids are colored red, inserted amino acids are colored olive drab, and deleted amino acids are colored teal. The amino acids at both ends of the key amino acid sites that are missing in the atomic model of DH1052 are marked. The structure figures were prepared using ChimeraX (http://www.cgl.ucsf.edu/chimerax)