Extended Data Fig. 10. Conformational changes in the converter.

a, Side-by-side comparison of the atomic models corresponding to the RuvB motors states in the nucleotide cycle (s1-s5) and the initiation states (s0^-A, s0) obtained from dataset t2. b, A hydrophobic interaction of RuvA^D3 is established with α -helix α3 and the presensor-1 β hairpin of RuvB subunit D or E. Surface representation of RuvB with hydrophilic amino acids shown in turquoise and hydrophobic residues shown in sepia. A cartoon model of only one RuvA^D3 is shown. c, Motion analysis of RuvB subunits D and E focused on the RuvA^D3 binding interface highlighting the wedge-like effect. Arrows indicate the magnitude and directionality of the motion between matching C_α-atom pairs. d, Domain rearrangements associated with nucleotide exchange in cluster [D] in the transition from state s1 to s2 (ADP→apo). Nucleotides are shown in surface representation and highlighted in red. To visualise the motions, RuvB subunits were superimposed on the head domain of subunit D. e, Unidirectional motion of subunits F with respect to RuvB subunits A during the nucleotide cycle. The largest motion occurs in the transition from state s4 (yellow) to s5 (red), when the ATP hydrolysis reaction is completed and the Mg²⁺ has dissociated from the ADP in the nucleotide binding pocket of RuvB subunit A. f, Opening motion of the RuvB subunit E N-terminus during the progression of the nucleotide cycle. Note that the opening motion is mainly visible in cluster [E]. g, Superposition analysis of the nucleotide exchange facilitating RuvB_D subunits from states s2, s3 and s4. A low average RMSD_Ø of 0.3 Å reveals that subunits RuvB D remain almost invariable during the three APO states. h, Position of the converter in the RuvB motor. The converter consists of RuvB subunits E and F together with the large ATPase domain of subunit D (all shown in pink). The converter connects the ATP-hydrolysing nucleotide binding pocket of RuvB subunit A with the nucleotide-exchanging nucleotide binding pocket of subunit D. Lines indicate the downwards-directed motion of the converter during the nucleotide cycle. i, Closing motion of the RuvB subunit D N-terminus during the progression of the nucleotide cycle. Note that the closing motion is associated with the acquisition of a new ATP molecule and can therefore only be observed in subunits D. Since the opening and closing of the RuvB N-terminus take place over three RuvB conformational clusters ([F], [E] and [D]), these motions occur over three translocation steps/nucleotide cycles. j, Domain rearrangements associated with nucleotide exchange in cluster [D] in the transition from state s4 to s5 (apo→ATP). Nucleotides are shown in surface representation and highlighted in red. To visualize the motions, RuvB subunits were superimposed on the head domain. k, Structural plasticity between all RuvB motor states obtained in this study (t1 and t2 dataset). States were aligned to the DNA. Colours indicate the RMSD (in Å). In the top panel, initiation state s0 served as a reference. The two most similar states are the states s0_t1 (boxed) and the RuvA^D3-free state s0^-A, obtained from RuvB-HJ particles. In the lower panel, nucleotide cycle state s1 served as a reference. The most similar state is s1_t1 (boxed). In both cases, the comparison with states s2 to s5 highlights that those motions of RuvB subunits are largest restricted to the converter.