Fig. 1. Architectures of the substrate-bound Lon^ENZ and substrate-free, Lon^OFF configurations.

(A) Cutaway view of the substrate-bound Y. pestis Lon^ENZ atomic model (center) flanked by orthogonal exterior views of the ATPase (left) and protease (right) domain rings. Each subunit of the homohexamer is assigned a distinct color depending on its position in the spiral staircase, and the cryo-EM density of the substrate is shown as a solid isosurface colored orange. Nucleotides are depicted using a sphere representation. (B) The different orientations of individual protomers relative to the protease domain, produced by orienting all the protease domains to a common view. Subunits are colored as in (A). The descending and ascending movements of the NTD^3H and ATPase domains relative to their proteases are accentuated by dashed lines shown above the NTD^3H. Dihedral angle measurements between ATPase and protease domains demonstrate a gradual expansion of descending subunits in the spiral staircase and compression in the two seam subunits. (C) Cutaway view of the substrate-free Y. pestis Lon^OFF atomic model (center) flanked by orthogonal exterior views of the ATPase (left) and protease (right) domain rings. Subunits are colored to correspond to their position in the Lon^ENZ staircase architecture after transitioning. Nucleotides are depicted using a sphere representation. (D) The similar orientations of the individual protomers of the substrate-free structure are produced by orienting all the protease domains to a common view without changing axial position. The descending movement of the subunits is accentuated by dashed lines shown above the NTD^3H. Dihedral angle measurements between ATPase and protease domains demonstrate subtle changes in the expansion and compression of the six descending subunits.