Supplementary Figure 9: Molecular-replacement model and omit map.

a, Two views of the EM density used as a molecular replacement model to solve the structure of the crystallized Npl4 fragment. The arrow indicates the extra density attributed to Ufd1, which does not reappear in the crystal structure. b, A simulated annealing composite omit map was calculated to assess model bias from the EM density map. The map is displayed at 1.0 σ with a carve of 1.8Å. Shown is the fit of the model into the density of the first Zn²⁺-finger domain. Arrows indicate residues whose side chains are not well represented in the map due to conformational flexibility. The red sphere indicates the zinc atom. c, As in b, but for the region of the second Zn²⁺ finger. d, As in b, but for the region of the β-strand finger. e, A second cofactor molecule cannot be fit above the ATPase ring, as there are significant clashes between the two Npl4 molecules (in blue and brown).