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. 2022 Jun 14;55(6):1105–1117.e4. doi: 10.1016/j.immuni.2022.03.019

Figure 5.

Figure 5

Two recurring SHMs synergistically drive the affinity maturation of a IGHV1-58/IGKV3-20 public clonotype

(A) An overall view of SARS-CoV-2 RBD in complex with the IGHV1-58/IGKV3-20 antibody PDI 222 (PDB 7RR0) (Wheatley et al., 2021). The RBD is shown in white, while the heavy and light chains of the antibody are in dark and light green, respectively. The ridge region (residues 471–491) is shown in pink.

(B and C) Structural comparison between two IGHV1-58/IGKV3-20 antibodies that either (B) carry germline residues VL S29/G92 (COVOX-253, PDB 7BEN) (Dejnirattisai et al., 2021) and (C) somatically hypermutated residues VL R29/D92 (PDI 222, PDB 7RR0) (Wheatley et al., 2021). SARS-CoV-2 RBD is in white, while antibodies are in yellow (COVOX-253) and green (PDI 222). Somatically mutated residues are labeled with bold and italic letters. The T-shaped π-π stacking between RBD-F486 and VL Y32 is indicated by a purple dashed line. Hydrogen bond and salt bridge are represented by black dashed lines.

(D) Binding kinetics between COVOX-253 Fabs (wild type or mutants) and SARS-CoV-2 RBD were measured by biolayer interferometry (BLI). y axis represents the response. Blue lines represent the response curves and red lines represent the 1:1 binding model. Binding kinetics were measured for five concentrations of the RBDs at 3-fold dilution ranging from 300 to 3.7 nM. The dissociation constant (KD) values ± standard deviations are indicated.

(E) A phylogenetic tree was constructed for the light-chain sequences of 67 antibodies in the IGHV1-58/IGKV3-20 public clonotype. The phylogenetic tree was rooted using the germline sequence of IGKV3-20. Each tip represents one antibody and is colored according to the corresponding amino acid variants at VL residues 29 and 92. Amino acid variants that represent SHM are underlined. Numbers of antibodies in the IGHV1-58/IGKV3-20 public clonotype carrying the germline-encoded variant at VL residues 29 and 92 (S29, G92), as well as VL SHM S29R and G92D (red) are listed in the inset table. Of note, one antibody in this IGHV1-58/IGKV3-20 public clonotype carries S29/N92 and another carries S29/V92. However, they are not listed in the table here.