Fig. 3: Interactions by conserved VIM, UBX and PUB domains of UBXD1 across the p97 hexamer.

a, Sharpened map of the P1 NTD (dark blue) and the VIM helix (brown) from p97–UBXD1^closed. b, Corresponding model showing VIM helix interactions with the NTD, colored as in a, with labeled interacting residues. c, Sharpened map of the P6 NTD (light blue) and UBX domain (yellow) from p97–UBXD1^closed. d,e, Corresponding model of the UBX and NTD showing a conserved orientation of the S3/S4 loop⁴⁵ (arrow) (d) and non-canonical structural elements Uα2, Uα3 and Uβ0 (e), colored as in c. The N-terminal (Nn) and C-terminal (Nc) lobes of the NTD are indicated. f, Overlay of PUB domains from p97–UBXD1-PUB_in (gray) and p97–UBXD1-PUB_out (white), aligned to the UBX (yellow) domain, showing 46° rotation of the PUB domain position. g,h, Low-pass filtered map and model of p97–UBXD1-PUB_in depicting PUB domain contact with p97 and model for C-terminal HbYX tail interaction from the adjacent P5 protomer (arrow) (g) and bottom view of the hexamer map with ‘out’ (white) and ‘in’ (gray) positions of the PUB (h). i, Cartoon of p97–UBXD1^closed depicting UBXD1 interactions across three p97 protomers (P1–VIM, P6–UBX and P5–PUB) through canonical p97-interacting domains.