(A) Ku-band (17.3 GHz) DEER signals at representative sites illustrating the change in the signal induced by the transition from the apo state to the ADP/Vi intermediate. (B) In this transition, distance distributions P(r) for sites 539 and 248 become narrow, with average distances showing large negative shifts; whereas for site 61, the shift is large and positive. Time-domain DEER signals and details of distance analysis are further illustrated in Figures S1–S5 supplementary material. The broad distance distribution at site 61 indicates a highly flexible loop. The distance change at this site in liposomes (even though it is very similar to that in detergent) may indicate a shift in the relative population in a bimodal distribution (Figure S1) although further work would be required to substantiate this result. In the samples of ADP/Vi intermediates, a small fraction of MsbA in the apo state is also present; and as a result, a low-intensity component in the P(r), corresponding to this state, is visible in this case and is larger in lipid. (These satellites are suppressed for sites 248 and 539 in (B).) For site 61, the lines overlap and are displayed as is, but they are shown separated in the supplement. a-ddm: alpha dodecyl maltoside.

(A) Ribbon representation of Sav1866 structure highlighting sites of spin labeling using the numbering scheme of MsbA. (B) Locations of labeling sites 57, 60, and 61 in the ECL1 loop on the periplasmic side of Sav1866. (C) Relative orientations of sites 248 and 301 in a close up view through the closed chamber at the cytoplasmic side. The front helices are deleted to open the view of the two residues. (D) Top view of the NBDs in Sav1866 highlighting the location of 539.

(A) Biphasic increase in distance between chamber-facing residues. The onset of the monotonic phase depends on the solubilizing detergent. Udm: undecyl-maltoside. (B) High concentration of LPS induces the appearance of a mobile component in the ESR spectral lineshape. (C) A population of transporters with an increased separation between monomers as reflected in the P(r) at site 301. This effect is inhibited by prior formation of the ADP/Vi intermediate. Subsequent ATP hydrolysis only partially restores the original lineshape. ESR samples were in 0.08% α-ddm.

The cartoon recapitulates the domain swapping and twisting that characterizes the structure of Sav1866 (ADP/Vi intermediate) [13]. The apo intermediate has large separations between the two NBDs (Figure 1) which leads to high accessibility to the polar reagent NiEDDA on the cytoplasmic side as reported by Dong et al. [29]. Transition to the ADP/Vi intermediate reduces accessibilities and distances on this side of the transporter.