A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein

M. Gordon Joyce; Rajeshwer S. Sankhala; Wei-Hung Chen; Misook Choe; Hongjun Bai; Agnes Hajduczki; Lianying Yan; Spencer L. Sterling; Caroline E. Peterson; Ethan C. Green; Clayton Smith; Natalia de Val; Mihret Amare; Paul Scott; Eric D. Laing; Christopher C. Broder; Morgane Rolland; Nelson L. Michael; Kayvon Modjarrad

To determine the structure of CR3022 in complex with the SARS-CoV-2 RBD, we carried out crystallization conditions screening, with crystals of the CR3022-RBD complex forming in 1M Succinic acid, 0.1M Hepes pH 7, 2% PEG MME2000 and determined the crystal structure by X-ray diffraction to 4.25 Ã… ( Table 1 ). The complex structure was solved by molecular replacement using the refined CR3022 and SARS-CoV-2 RBD structures as search models and was refined to an Rwork/Rfree of 0.242/0.292 (Table 1) . CR3022 bound to the RBD at an epitope centered on S glycoprotein residues 377-386 with a total buried surface area of 871 Ã… (Figure 3, Figure S2 , and Table S1 ). This region is highly conserved between SARS-CoV and SARS-CoV-2 ( Figure S3) . Comparison of the CR3022 epitope site with previously described antibody-complex structures for SARS-CoV, and MERS-CoV indicates that CR3022 describes a novel recognition site (Figure 3 and Figs. S3, S4) . Further sequence analysis of the epitope indicates that this epitope is conserved in betacoronavirus clade 2b, with also some similarity in clade 2d (Fig. S3) . To confirm a CC0 license. author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under The copyright holder for this preprint (which was not peer-reviewed) is the . that this site was also shared with 240CD, we produced an RBD knockout mutant by introducing a glycan sequon at position 384, and by biolayer interferometry show that both CR3022 and 240CD binding to the RBD can be eliminated by the introduction of a glycan at this site (Fig. S2D ).