Fig. 2: Structures of the conditional scFv P02_D09 were determined with or without MTX.
From: Direct control of CAR T cells through small molecule-regulated antibodies
a Comparison with the previous VHH structure bound to MTX (PDB code: 3QXV) demonstrates the presence of the light chain does not significantly perturb the MTX binding site. Structures are shown in cartoon rendering with scFv framework in deep teal, CDRHs 1, 2, and 3 shown in blue, yellow, and orange, respectively, CDRLs 1, 2, and 3 shown in red, green, and cyan, respectively, and MTX shown as magenta sticks. VHH + MTX is shown in a black cartoon with MTX as purple sticks. b A more detailed view of MTX bound to the conditional scFv shows MTX sitting underneath CDRH1 while also interacting with FW3. Residues contacting MTX are noted in the figure. c Alignment of the apo scFv structure (deep blue, HC and light blue, LC) with parental antibody M2J1 (deep olive, HC and light orange, LC) highlighting the interface between VH and VL. Side chains of mutations that revert the original VHH sequence back to the M2J1 sequence to stabilize the interface are shown as sticks. d Zoomed in view of the transition between apo and MTX-bound scFv P02_D09 highlighting the inward flip of W32 in CDRH1 upon MTX binding and the corresponding movement of D102 in CDRH3. Structures are shown as cartoon and colored as in (a) with noted side chains and MTX shown as sticks.
