(A) Ribbon presentation of a modeled Hsp104 hexamer that was constructed from the L/S* rigid body of the crystallized filament. The dimensions of the Hsp104 hexamer are indicated and subunits are colored as in Figure 1B). (B) Ribbon representation of the proteasomal Rpt1-6 present in two alternative conformations (state-1, PDB 4cr2, orange, and state-2, PDB 4cr4, green (Unverdorben et al., 2014)). The two AAA rings are shown together with the MD belt (grey surface) of the superimposed Hsp104 hexamer. Conformational differences between the Rpt1-6 ATPase modules are indicated. The asterisk highlights a hypothetical clash with the MD belt. (C) Ribbon presentation of the modeled Hsp104 hexamer highlighting the L/S* rigid bodies (colored differently). The different numbers of identified Lys-Lys cross-links are represented by intermolecular connections, linking neighboring rigid bodies (wt in black, E450A in blue, K494A in red). The proposed effects of activating and repressing mutations on the dynamics of the Hsp104 hexamer are schematically indicated. See also Figure 4—figure supplements 1 and 2.