Fig. 3: Crystal structures and epitope of three representative nanobodies bound to SARS-CoV-2 RBD or SARS-CoV-1 RBD.

a, d Crystal structures of 1-2C7 and 3-2A2-4 bound to SARS-CoV-2 Beta and prototype RBD, respectively. b Crystal structure of Nb70 and 1F11 bound to SARS-CoV-2 prototype RBD. SARS-CoV-2 RBD is colored in cyan whereas 1-2C7 in orange, Nb70 in green, and 3-2A2-4 in purple. c Crystal structure of Nb70 bound to SARS-CoV-1 RBD. Nb70 is shown in green while the SARS-CoV-1 RBD in blue. e, h The epitope of 1-2C7 (orange) or of 3-2A2-4 (purple) is respectively depicted on the surface of SARS-CoV-2 RBD. f The epitope of Nb70 (green) depicted on the surface of SARS-CoV-2 RBD or g on the SARS-CoV-1 RBD. The same residues between SARS-CoV-2 and SARS-CoV-1 epitopes were underlined. The epitope of CR3022 highlighted in red (PDB: 6YM0 on SARS-CoV-2 RBD and PDB: 7JN5 on SARS-CoV-1 RBD) is superposed onto that of e 1-2C7 and f Nb70 on SARS-CoV-2 RBD, or onto g Nb70 together with that of VHH72 in white on SARS-CoV-1 RBD (PDB: 6WAQ). h The epitope of S309 in yellow (PDB: 7R6W) is superimposed onto that of 3-2A2-4. i Interactions between 1-2C7 and SARS-CoV-2 Beta RBD, j between 3-2A2-4 and SARS-CoV-2 RBD with hydrophobic pocket residues of RBD in light blue., k between Nb70 and SARS-CoV-2 RBD, and l between Nb70 and SARS-CoV-1 RBD. Levels of residue conservation among m over 8 million SARS-CoV-2 RBD sequences and n 46 sarbecovirus RBD sequences from GISAID database collected from December 2019 to June 2022. The white surface represents conserved residues, whereas green in m or purple in n represents variable residues. Several key residues responsible for antibody escape were indicated with levels of conservation. The epitope of ACE2 is outlined in black and the epitope of 1-2C7 is outlined in orange whereas Nb70 in green and 3-2A2-4 in purple.