Fig. 2: Three conformational states of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos.

Single-particle cryo-EM maps (unsharpened, 0.009 threshold) of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos. Three conformational states were resolved using 3D classification. Each state is in a similar conformation to one of the states in the complex of p97 and Npl4/Ufd1 without the substrate (compare to Fig. 1b). One ubiquitin molecule (pink) was observed to bind to the top of Npl4. One of the N domains in State III (dark gray) shifted and interacted with ZF1 (zoomed in Supplementary Fig. 4b). The color scheme used for the other domains is the same as that used in Fig. 1. The position of Npl4 relative to p97 is illustrated in the cartoons. Unresolved linkers between UBXL and ZF1 are represented by dotted lines. The central pore of the D1 ring in State III is highlighted by an arrowhead. The conserved groove of Npl4 that was found to bind an unfolded ubiquitin in the yeast complex structure¹⁴ was marked by a green band in State III.