Extended Data Fig. 5: SdeA(231–1190) binds three Ub molecules.

a, Overall structure of the SdeA(231–1190)–Ub complex. SdeA is coloured as in Fig. 1b. The three Ub molecules are coloured in magenta and labelled as Ub1–3 according to the order of their binding region in SdeA(231–1190). Q935 and S998, which are two common C termini of the clones used in this study, are shown as spheres. b, Ub binding causes prominent structural changes of SdeA. The SdeA–Ub complex structure is shown as in a, and the apo-SdeA structure is coloured in pink. The N-terminal region of SdeA pCTD which undergoes pronounced conformational changes is outlined with a circle. c, d, Expanded views of the two Ub binding sites in SdeA pCTD. The proteins are coloured as in a. Red dashed lines indicate polar interactions. e–h, Structural alignments of the Ub molecule (magenta) in the SdeA mART–Ub complex with the proximal (yellow) and distal (orange) Ubs of the K11- (e), K48- (f), K63- (g) and M1-linked (h) diubiquitins. The two R42 residues in each of the four diUbs are shown in stick representation.