Extended Data Fig. 7: Substrate engagement by USP deubiquitinases.

a. Cartoon representations of covalent USP-Ub/Ubl substrate complexes of USP7~Ubiquitin-aldehyde (left, PDB-ID: 1NBF), USP36~Fubi-PA (second to left), USP36~Ub-PA (second to right) and superposition of these three structures (right). Distinct conformations in the switching loops and in blocking loops 1 are highlighted. b. Zoom-in on the palm/thumb cleft of USP36 in the USP36~Fubi-PA structure, which guides the C-terminal tail of Fubi towards the active site Cys131. Hydrogen bonds are indicated with dotted lines. Gln206 of the switching loop contacts the blocking loop 2 backbone and thereby forms a narrow substrate channel, which is responsible for restricting cleavage activity to a terminal diGly motif. c. Zoom-in on the hydrophobic anchoring of the switching loop in USP36 on the α5 helix, stabilizing recognition of Fubi Pro47 by Tyr215 in USP36. d. Cartoon representation of the USP36~Fubi-PA structure with all waters which are within 5 Å of both proteins shown as red spheres. The large presence of water in the USP36-Fubi interface is typical for USP deubiquitinases⁵² and indicates numerous polar contacts. e. Cartoon representation as in d for the USP36~Ubiquitin-PA structure.