Extended Data Fig. 6: Specific recognition of Ub by SdeA mART.

a, The interaction between SdeA mART and Ub. SdeA mART is shown as a surface electrostatic potential model and Ub is in magenta cartoon representation. The R42, R72 and R74 residues of Ub are shown in stick representation. b, Ub^R72 and Ub^R74 are bound in the negatively charged groove of SdeA mART. The front part of SdeA mART is cut away to reveal the inner surface. c, Superimposition of SUMO1 (PDB: 1WM3), NEDD8 (PDB: 1NDD) and Ub in the SdeA mART-Ub complex. The conserved Arg residues in Ub, SUMO1 and NEDD8 are shown in stick representation, out of which Ub^R42, Ub^R72, and Ub^R74 are marked. The polar interactions with Ub^R72 and Ub^R74 are shown as red dashed lines. d, The purified SUMO and NEDD8 proteins were incubated with SdeA(193–935)^H277A and NAD⁺ under the conditions stated in the ‘Top-down LC–MS analysis of modified Ub and Ub-like proteins’ section of the Methods. Mass spectra of the samples are also shown. The sample names and their molecular masses are indicated in the figures. Similar results were obtained in three independent experiments.