Figure 4

Amino acid sequence and STAMP structural alignments of the RBD of SARS-CoV and SARS-CoV-2 compared to a predicted 3D structure of the RBD of RhGB01 highlighting structural differences in regions housing hACE2 contact residues for SARS-CoV and SARS-CoV-2. Contact residues are described in the literature (black), with residues in red the most identified residues. Regions coloured in purple have high structural similarity (> 0.7) and residues with a low structural similarity coloured in red/white (< 0.3). BM48-31 is included as comparison to a second Sarbecovirus from a bat source. (A) STAMP alignment of SARS-CoV-2 RBD (PDB ID 6M0J) in the conformation of being complexed with hACE2 aligned with the RhGB01 RBD. The areas where structural similarity is low are seen to contain contact residues defined in the literature. (B) Sequence alignment of RhGB01 and SARS-CoV-2. The sequence used is identical to (C). (C) Sequence alignment of the RBM with 28 residues up and downstream, to facilitate the inclusion of K417. The coordinates provided refer the SARS-CoV-2 (NC_45512.2) residue position within the spike protein alignment. (D) STAMP alignment of SARS-CoV RBD (PBD ID 2DD8) aligned with the predicted RhGB01 RBD. The region highlighted in green are residues upstream and downstream of the structural alignment which do not align. (E) Sequence alignment of RhGB01 and SARS-CoV. (F) Sequence alignment of RBM with SARS-CoV contact residues highlighted, and the coordinates provided refer to the residue position for SARS-CoV (NC_004718.3) within the spike protein alignment. 28 residues are included up and downstream of the RBM to include V404.