Figure 7. Peptide binding and mechanism of translocation.
(A) The pore loop 1 residues of subunits A-D form a helix (axis, black line) that matches the symmetry of a canonical twisted β-strand, which rotates 60° and translates 6.3 Å every two residues. In white are the positions that subunits E and F would adopt if they continued this helix. The three positions seen for subunit F (Figure 2—figure supplements 7–8) appear to be snapshots along the return path from the end of the helix at subunit E to the start of the helix at subunit A. (B) Steps along the translocation cycle inferred from the cryo-EM structure. The peptide shown is modeled as a β-strand along the helix axis of subunits A-D. Vps4 maintains a constant interaction with the peptide through steps 1 to 4 before dissociating at step 5 and rebinding 12 residues further up the peptide at step 7, which is equivalent to step 1. Nucleotides suggested by density and coordination geometry are labeled. Pore loop 1 contacts with the substrate peptide in steps 1–4 are indicated with an asterisk. The two subunits closest to the view direction are included with 50% transparency. The two horizontal lines are separated by 37.8 Å (12 residues) and indicate points of substrate contact with pore loop 1 of the highlighted subunit.
Figure 7—figure supplement 1. Comparison of the Vps4 hexamer with the ATPases of the 26S proteasome.
Figure 7—figure supplement 2. Comparison of the Vps4 hexamer with the NSF D1 ring.
