Figure 2. ClpX-degron interactions.

(A) Positions of the RKH loop (blue), pore-1 loop (red), and pore-2 loop (green) in subunit A of the ClpX hexamer in the recognition complex relative to the positions of the ssrA degron (orange/gold). (B) Cutaway views of the recognition complex (left) and intermediate complex (right). In the recognition complex, the pore-2 loop of ClpX subunit A (denoted by red arrows) blocks the axial pore. The pore is open in the intermediate complex. (C) Key ClpX residues (blue or purple) and the C-terminal segment of the ssrA degron (gold) in the recognition complex are shown in stick representation. Dashed lines indicate hydrogen bonds. (D) ClpX-degron contacts in the recognition and intermediate complexes. ClpX or degron residues are shown in stick representation with semi-transparent density. (E) Subunit nucleotide state and degron/pore-loop interactions in the recognition and intermediate complexes.

Figure 2—figure supplement 1. Detailed contacts between ClpX and the ssrA degron.

(A) Schematic representation of recognition-complex contacts between ClpX side chains and the ssrA degron prepared using LigPlot (Wallace et al., 1995). Dashed lines indicate hydrogen bonds. Hydrophobic and van der Waal’s contacts are indicated by arcs with spokes. (B) LigPlot schematic of ClpX-degron contacts in the intermediate complex. (C, D) Surface area buried in the recognition or intermediate complexes between the ssrA degron and ClpX residues (X-axis) for different ClpX subunits (Y-axis).

Figure 2—figure supplement 2. Nucleotide density in subunits of the recognition complex (top) and the intermediate complex (bottom).