Fig. 3: Ternary complex characterization using CRBNmidi.
From: Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders
a–c Crystal structure of CRBNmidi in complex with mezigdomide and IKZF1ZF2. a CRBNmidi is shown in surface representation, mezigdomide is shown as black sticks and IKZF1ZF2 is shown as blue cartoon. b Superposition of the CRBNmidi:mezigdomide:IKZF1ZF2 crystal structure (coloured as in A) with the cryo-EM structure of CRBN:DDB1:mezigdomide:IKZF1ZF1-2-3 (PDB ID: 8D7Z, grey, DDB1 not shown). Polder OMIT (Fo-Fc) map of mezigdomide in protomers A and B contoured to 3 σ is shown in the inset. c Close-up of the ligand-protein and protein-protein interaction network inb. Hydrogen bonding interactions in the CRBNmidi:mezigdomide:IKZF1ZF2 interface are shown as blue dashed lines. d-g Crystal structure of CRBNmidi in complex with CFT-1297 and BRD4BD2. d CRBNmidi is shown in surface representation, CFT-1297 is shown as black sticks and BRD4BD2 is shown as blue cartoon. e The two protomers in the asymmetric unit, chain A coloured, chain B in grey. Polder (OMIT) (Fo-Fc) map of CFT-1297 in chains A and B contoured to 3 σ shown in the inset. f Close-up of the interface between BRD4BD2 (chain B) and CRBNmidi, residues Tyr372BRD4 and Gln390CRBN are shown as sticks with a likely hydrogen bond shown as a blue dashed line. g Chemical structure of CFT-1297. h TR-FRET traces monitoring ternary complex formation of BRD4BD2 and different constructs of CRBN in the presence of a dilution series of CFT-1297. i CRBNmidi-on-chip SPR sensograms measuring binding of CFT-1297 alone (left) and CFT-1297 pre-incubated with BRD4BD2 (right).
