The binding epitope is crucial for HER3-targeting antibody to block ligand binding, heterodimerization, and HER3 uptake
6. DB-1310 bound to a unique epitope on HER3 that is distinct from the epitopes recognized by patritumab and elgemtumab (
Figure S2A). The cryo-EM structure of the DB-1310 Fab fragment binding to the HER3 extracellular domain (HER3-ECD) with a maximal resolution of 3.29 Å revealed that DB-1310 extensively interacts with domain I of the HER3-ECD. Moreover, the DB-1310 Fab fragment binding to the HER3-ECD was shown to be spatially separated from the ligand-binding site located between domains I and III, and the HER2/HER3 dimerization interface of domain II (
Figure S2B). The observed interface included hydrogen bonds and ionic interactions between the HER3 residue (S128, R132, D153, C156, R181, and S182) and the heavy chain (S50, Y53, Y70, Y73, D118, D120, and Y121) or the HER3 residue (S95, T96, and R132) and the light chain (Y51, G110, and D111;
Figure S2C-E). DB-1310 demonstrated partial blocking of NRG-1 to HER3 despite the non-overlapping binding site with the ligand, NRG-1 (
Figure S2F, G). These data indicated that DB-1310 binds a unique epitope of HER3-ECD domain I with a potential allosteric effect on receptor function.