Fig. 2: Structure of the hNEMO-bound 3CLpro C145S homodimer.

a The hNEMO_226–234-bound 3CLpro dimer. N- (NH3 + ) and C-termini (COO-) are labeled. hNEMO_226–234 (NEMO B - orange) binds into chain B (purple) and is surrounded by an omit map of electron density (1.0 σ contour level and 1.9 Å carving radius). Acetylated Lys226 and Tyr234 at the N- and C-termini of the hNEMO_226–234 peptide, respectively, are labeled. The C-terminal tail of chain D (teal) from a crystallographic symmetry equivalent binds into the substrate-binding site of chain A (light pink). Domains I, II and III are labeled. b Structure of the hNEMO-bound C145S variant asymmetric unit. The C-terminal tail of chain A (pink) binds into the substrate-binding site of chain D (teal). hNEMO peptides bound into chain B (purple) (NEMO B - orange) and chain C (light blue) (NEMO C - wheat) are superimposed with an omit map (1.0 σ contour level and 1.9 Å carving radius) of their electron density. c Interactions of hNEMO_226–234 with the substrate-binding groove of 3CLpro C145S. hNEMO_226–234 is colored orange. Residues Lys226 to Tyr234 are fully labeled. The surface of chain B (purple) is shown. Substrate-binding residues in chain B are portrayed as sticks and labeled. Catalytically relevant residues are labeled in bold. Hydrogen bonds are depicted as dashed yellow lines. The hydrogen bond predicted to form between Cys145 (in WT) or Ser145 (in C145S) and His41 is depicted as a dashed green line. d Interactions of the C-terminal tail of chain A with the substrate-binding groove of 3CLpro C145S. The C-terminal tail of chain A is colored light pink. Residues Ser301 to Gln306 are fully labeled. The surface of chain D (teal) is shown. Interacting residues and their interactions are portrayed as in c. The oxygen atom of water 109 is depicted (red sphere). e The C-terminal tail at the 3CLpro dimer interface. The C-terminal tail of chain B (purple) is depicted as sticks, juxtaposed over its cartoon representation. Density from the omit map (1.0 σ contour level and 1.9 Å carving radius) is shown around the C-terminal tail. Arg298 to Phe305 and residues that interact with the C-terminal tail of chain B are labeled. Inset, schematic of chains A and B, showing the position of the C-terminal tail at the 3CLpro dimer interface.