a Overall structure of the yNpl4–yUfd1 complex in two orientations. b Close-up view of the interaction between yNpl4 and yUfd1. Hydrogen bonds are shown as black dotted lines. c Sequence alignment of the NBM region of Ufd1. The position of the β-strand in the NBM region in the yNpl4–yUfd1 structure is shown above the sequences. d Comparison of the MPN region of the yNpl4–yUfd1 and Rpn8–Rpn11–Ub (PDB 5U4P [https://doi.org/10.2210/pdb5u4p/pdb])25 complexes. The coloring scheme of the yNpl4–yUfd1 complex is the same as that in Fig. 3a. Rpn8, Rpn11, and Ub of the Rpn8–Rpn11–Ub complex are blue, orange, and pink, respectively. Hydrogen bonds are shown as black dotted lines. e, f Analysis of the binding between GST-yNpl4 and yUfd1 alone (e) or yUfd1–Cdc48 (f) by pulldown assays. The results from the triple mutant of yNpl4 (L296A L353A Y424) (left) or the triple mutant of yUfd1 (G297R L299A F301A) (right) are shown. In all, 20% input means 20% of the volume of the sample (yUfd1 and/or Cdc48) that was mixed with the GST-yNpl4-bound glutathione resin. Asterisks indicate contamination. The bound proteins were analyzed by SDS-PAGE and stained with Coomassie brilliant blue. Source data are provided as a Source Data file.