Fig. 6: SHM contributed to hydrogen bonds between NCV2SG53 and E484 residue of RBD.
From: Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants
a Interaction of RBD E484 residue with NCV2SG53 mAb through the multiple hydrogen bonds. Among hydrogen bonds formed on RBD E484, S57 residue in the NCV2SG53 heavy chain CDR2 was generated by the SHM and contributes to increased binding affinity. b NCV2SG53-RBD binding interface on the Wuhan RBD surface model. Residues forming a hydrogen bond with HC (blue) and LC (green) are indicated. Hydrogen bonds generated by SHM (red) are shown on the binding interface (pink). The ACE2-binding site is surrounded by a dotted line (cyan). c Comparison of the NCV2SG53 binding interface between Wuhan RBD and Delta RBD. The binding interface of HC (blue), LC (green), or HC/LC overlapped (yellow) is shown on the surface model of RBD. d The matrix represents amino acid substitutions present in RBD of indicated SARS-CoV-2 variants. The substituted amino acids are shown in red boxes. The numbers of hydrogen bonds of NCV2SG53 to Wuhan RBD are indicated on the corresponding amino acid residue. Residues of blue interact with SARS-CoV-2 RBD. E484 in RBD is the most important for binding with NCV2SG53 (pink). Mutation in the E484 residue of SARS-CoV-2 RBD reduces the binding of NCV2SG53. IC50 of neutralizing activity of NCV2SG53 to SARS-CoV-2 pseudoviruses is indicated (IC50: ++++, <10 ng/ml; ++, 100–999 ng/ml; −, >1000 ng/ml).
