Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class

Rapp, Micah; Guo, Yicheng; Reddem, Eswar R.; Liu, Lihong; Wang, Pengfei; Yu, Jian; Cerutti, Gabriele; Bimela, Jude; Bahna, Fabiana; Mannepalli, Seetha; Zhang, Baoshan; Kwong, Peter D.; Ho, David D.; Shapiro, Lawrence; Sheng, Zizhang

Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determined structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three utilized VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy chain N53I enhancing binding and light chain tyrosines recognizing F486RBD. Despite these similarities, class members bound both RBD-up and -down conformations of the spike, with a subset of antibodies utilizing elongated CDRH3s to recognize glycan N343 on a neighboring RBD – a quaternary interaction accommodated by an increase in RBD separation of up to 12 Å. The VH1-2-antibody class thus utilizes modular recognition encoded by modular genetic elements to effect potent neutralization, with VH-gene component specifying recognition of RBD and CDRH3 component specifying quaternary interactions. Highlights Determine structures of VH1-2-derived antibodies 2-43, 2-15, and H4 in complex with SARS-CoV-2 spike Define a multi-donor VH1-2-antibody class with modular components for RBD and quaternary recognition Reveal structural basis of RBD-up and RBD-down recognition within the class Show somatic hypermutations and avidity to be critical for potency Delineate changes in spike conformation induced by CDRH3-mediated quaternary recognition