Fig. 7: Structural analysis of p97–UBXD1 mutant complexes and model for p97 hexamer remodeling through UBXD1 domain interactions.
a, Table of ADP-bound p97–UBXD1 cryo-EM datasets (WT, LX and H4X) and corresponding UBXD1 domains observed as densities in the reconstructions. b, Unsharpened map and fitted model of the VIM–H4-bound P1 protomer from p97–UBXD1LX (Extended Data Fig. 9d), colored as in Fig. 1. c, First and last frames of the 3D variability analysis output for p97–UBXD1LX showing P6 D2 density (*) but no VIM–H4 in one end state (top) and no P6 D2 in the other when VIM–H4 density is present (bottom). d, P1–P6 interprotomer distances (based on centroid positions) for the D1 and D2 domains of p97ADP (PDB 5FTK), p97–UBXD1closed, p97–UBXD1LX, p97–UBXD1H4X and p97–UBXD1open. Dashed lines represent the minimal distances observed in p97ADP. A schematic representing the distances calculated is shown (right). e, Model of p97–UBXD1 interactions and structural remodeling of the hexamer. State I, side view of p97ADP (PDB 5FTK), colored as in Fig. 1. NTDs are shaded for clarity. State II, p97–UBXD1VIM, in which the VIM initially associates with the NTD of P1. The position of the D2 small subdomain is illustrated by α12′ and an adjacent helix. State III, the p97–UBXD1closed state, in which the UBX, PUB and helical lariat contact P1, P5 and P6, resulting in the disruption of D1–D1 contacts at the P1–P6 interface. State IV, the p97–UBXD1H4 state, in which H4 is positioned on top of the D2 domain of P1, causing it to rotate upward and displacing a helix from the D2 domain of P6. State V, the p97–UBXD1open state, in which P6 and P1 have completely separated and all protomers are arranged into a shallow right-handed helix. f, Summary of p97–UBXD1 interactions identified in this study.
