Extended Data Fig. 4: Hexamer remodeling in p97–UBXD1^closed and p97–UBXD1^open.

(a) Overlay of protomers P1 (dark blue) and P6 (light blue) from p97–UBXD1^closed, aligned to protomers P3 and P4 from PDB 5FTK. P1 and P6 protomers from 5FTK are shown in gray. (b) As in (a), but depicting p97–UBXD1^open protomers. (c) Side-by-side view of individual protomers aligned based on position in the p97–UBXD1^open hexamer, showing vertical displacement along the pseudo-C6 symmetry axis. (d) Overlay of the D1 (left) and D2 (right) AAA+ domains of P1 for p97^ADP, p97–UBXD1^closed, and p97–UBXD1^open, aligned to the large subdomains and colored as indicated. ADP is shown with conserved Walker A/B (green and purple, respectively) and trans-acting (P6) Arg finger residues indicated. The large rotation of the D2 small subdomain, exemplified by α12′, is shown (relative to p97^ADP) for the closed (1) and open (2) states. (e) Unsharpened map of the D2 domains of protomers P1 and P6 of p97–UBXD1^open, overlaid with the D2 domain from p97^ADP on P6, showing lack of density for helix α5′ (gray, encircled) normally contacting the counterclockwise D2 domain. The D2 domain of P1 of the open state is shown for clarity. (f) Top view overlay of the D1 (left) and D2 (right) domains for the P6-P1 pair in the three states and aligned to P1 to show relative rotations of P6, colored as indicated. Rotations shown are from p97^ADP to p97–UBXD1^open and determined from centroid positions of the D1 and D2 domains.