Fig. 3: HDX-MS, binding, and mutagenesis studies suggest an overlap between the MR3 epitope and RBM.

a Epitope mapping using HDX-MS. RBD residues are color-coded based on the extent of the solvent exchange as an indication of protection by MR3-binding. b MR3 competes with ACE2 for RBD binding. The RBM surface is highlighted in cyan. c–h MR3 competes with RBM-targeting antibodies for RBD binding. They include monoclonal antibodies CB6³⁵ (c), CV30³⁶ (d), REGN10987¹² (e), REGN10933¹² (f), and the two sybodies SR4 (g) and MR17 (h) characterized in this study. i The MR3-RBD binding is compatible with SR31, which targets a non-RBM surface³⁷. In c–h, the epitopes of the antibodies are highlighted in cyan except for SR4 and MR17, which are shown in Fig. 1c, e. In b–h, binding assays were performed using RBD immobilized on a sensor. BLI profiles were recorded with (black and blue) or without (red) pre-saturation of MR3 using the indicated antibodies as analytes. The assays in i were performed as in b–h except that SR31 was used for pre-saturation. j Three RBD mutations (red and blue) with severely impaired MR3 binding compared with the wild type (WT, black). The data for the rest of the 10 mutants are in Supplementary Fig. 9. k Mapping the mutagenesis data to the RBD structure. Residues are colored based on the sensitivity to alanine mutation; mutants showing <80% binding signal compared to the wild type are considered to be involved in binding, assuming no allosteric effects. Source data for b–j are provided as a Source data file. ACE2 angiotensin-converting enzyme 2, BLI biolayer interferometry, HDX-MS hydrogen–deuterium exchange mass spectrometry, RBD receptor-binding domain, RBM receptor-binding motif.