Fig. 3: Gid12 remodels the N-degron binding pocket in Gid4. | Nature Communications

Fig. 3: Gid12 remodels the N-degron binding pocket in Gid4.

From: Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation

Fig. 3

a Superposition of Gid12-bound Gid4 (gold) with prior structures of Gid4 from GIDSR4 complexes without substrate (“Apo”, PDB ID: 6SWY, purple) and bound to the Pro/N-degron of Fbp1 (PDB ID: 7NS3, cyan) reveals conformational heterogeneity of Gid4 L2-loop. b Closeup showing structural differences in Gid4 L2-loop when bound to Gid12 (Gid4 in gold) or to Pro/N-degron of Fbp1 substrate (Gid4 in cyan, PDB ID: 7NS3). c L2-loop structural similarity amongst human Gid4 structures with various N-degron peptides (PDB ID: 6CCT, 6CCU, 6CD8, 6CD9, 6CDC, 6CDG, 6WZX, 6WZZ; colored in cyan, pink, lawn green, salmon, gray, yellow, deep pink and blue respectively). Yeast Gid4 from apo GIDSR4 (6SWY) is shown in purple with its disordered L2-loop indicated with arrow and dotted line, and human Gid4 Leu164, which corresponds to yeast Gid4 Leu172, are shown for reference. d Closeups showing Gid4 L2-loop (gold) bound to Gid12 (blue), with Gid12 depicted as ribbon (left) or surface (right). The Gid4 L2-loop conformation complements the Gid12 pocket at the junction between blades 7 and 1 in the central pore.

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