Figure 7. Rearrangement of the spiral staircase upon substrate engagement.

(a) Cutaway side view of the Rpt ring in the substrate-free (left) and substrate-engaged (right) state, with Rpt6 and Rpt5 removed for clarity, respectively, and oriented with the top subunit of each spiral staircase on the left. Individually docked copies of the PAN crystal structure (ribbons, PDB ID: 3H4M) reveal different spiral staircase arrangements in the two states, which are emphasized by a sphere representation of the pore-loop residue that is predicted to drive translocation. (b) The AAA+ domains of Rpt1–Rpt6 are shown individually in the same orientation, with their pore loops facing right and the aromatic pore-loop residue shown in purple. In the absence of substrate, the entire AAA+ domains are rotated to varying degrees away from the central pore, leading to a pronounced spiral-staircase arrangement of large subdomains with a global pitch that is indicated by a continuous line. Substrate engagement arranges the AAA+ domains at a more uniform height, with a lower-pitch spiral staircase of pore loops established solely through varied tilting of the large subdomains (emphasized by black lines).