Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming a VL-VL dimer

Chimeric Antigen Receptor T-cell (CAR-T) immunotherapies are dependent upon designed transmembrane proteins to bind target antigens and stimulate an immune response. The success or failure of these CARs is only partially predictable, yet recent work has highlighted the importance of antigen binding scFvs driving distinct oligomerization states with varied CAR-T efficacy. Here, we sought to determine the extracellular structure of the anti-CD19 CAR 47G4-CD828Z. Unexpectedly, the resolved crystal structure revealed an IgVL homodimer bound along an inverted VL|VL interface. We found that the VL-VH linker, designed to be cleavage resistant, was cleaved, and the VH and CAR hinge domains were absent from the crystal structure lattice. Molecular Dynamics simulations revealed that the inverted VL|VL interface was more stable than the canonical VL|VL configuration. Our work substantiates the need to interrogate the scFv structure and CAR oligomerization state for optimal CAR-T design.