Fig. 5: Structure of the Drg1 hexamer in processing a peptide substrate.

a The atomic model of the NTD ring of the Drg1 hexamer in the substrate-processing state. The six protomers are indicated as P1 to P6. b The atomic model of the D1 ring shown in cartoon representation. The PLs (PL-I and PL-II) engaged with the substrate are shown and highlighted in zoom-in panels. c The atomic model of the D2 ring. The PLs (PL-I and PL-II) engaged with the substrate are shown and highlighted in zoom-in panels. d Side view of the Drg1 hexamer with a substrate engaged in the central channel. For clarification of the substrate, P1 and P6 are not shown. e The spiral configuration of the PLs of Drg1 protomers around the substrate in the central channel. The interaction patterns of the PL-Is and PL-IIs are shown in the left and right panels, respectively. The vertical distance of PLs between the lowest and highest protomers are shown as indicated. f The atomic interactions between the PL-Is and the substrate. The conserved PL-Is (K318-Y319-L320) of the D1 domains (left) from P2 to P5 are shown in the left panel, and the PL-Is (K589-Y590-V591) of the D2 domains from P1 to P5 are shown in the right panel. Both the atomic models and cryo-EM of the PL-Is are shown, and color-coded as indicated. g Sequence alignment of the ISS motifs from S. cerevisiae Cdc48, Drg1 and H. sapiens p97. h The ISS motifs in the D1 (left) and D2 (right) rings. The ISS motifs are color-coded, and the nucleotides are highlighted in purple sphere models. The ISS motifs of P3, P4, and P5 in the D1 ring, and P2, P3, P4, and P5 in the D2 ring form a stretched loop inserting into the neighboring nucleotide-binding site. i Conformations of the ISS motifs in representative tight/loose protomer interfaces of the D1 ring. The ISS motif of P2 in the D1 ring is in a retracted (helical) conformation, whereas the P4 ISS motif in the D1 ring is in a stretched loop conformation. j Same as i for the ISS motifs in the D2 ring.