a, Local resolution of the cryo-EM map of vanadate-trapped LptB 2 FG. b, FSC curves: gold-standard FSC curve between the two half maps with indicated resolution at FSC = 0.143 (red); FSC curve between the atomic model and the final map with indicated resolution at FSC = 0.5 (blue); FSC between half map 1 (orange) or half map 2 (green) and the atomic model refined against half map 1. c, Cutaway views of angular distribution of particles included in the final 3D reconstructions of vanadate-trapped LptB 2 FG (top) and LptB 2 FGC (bottom). d, As in a, except for vanadate-trapped LptB 2 FGC. e, As in b, except for vanadate-trapped LptB 2 FGC. f, Representative 2D class averages (top) and slices of 3D reconstructions (bottom) of nucleotide-free (left) and vanadate-trapped (right) LptB 2 FG. LPS density is indicated with a green arrow. These two slices are the same as the bottom slice in Extended Data Fig. 3d and the bottom slice in h. g, Cryo-EM densities with the atomic models for individual transmembrane helices in the vanadate-trapped LptB 2 FG. h, Cryo-EM map of vanadate-trapped LptB 2 FG filtered to 6 Å resolution to show the overall arrangement of the transmembrane helices and LptB subunits. Slices through the 3D map at the indicated planes show the positions of individual transmembrane helices and the collapse of the inner cavity (left). Overlays of the TMDs of LptF or LptG in the nucleotide-free (grey) and vanadate-trapped (blue and orange) LptB 2 FG show only small differences within each TMD (right). Red arrow indicates the bending of TM1 LptF upon nucleotide binding. i, Cryo-EM densities for the ADP–vanadate complexes trapped at the two ATP-binding sites between the LptB subunits in LptB 2 FGC and LptB 2 FG. The Walker A and signature motifs are coloured in grey and red, respectively. j, Proposed model for LptB 2 FGC-driven LPS extraction. The Lpt proteins are coloured as in Fig. 3a. Three β-jellyroll domains, the TM LptC and the LptC linker are labelled. LPS is depicted as a cartoon model of lipid A with the inner core. The TM LptC and LptC linker are shown as dashed lines in steps 3 to 5 to indicate their increased mobility. The ATP molecule, before or after hydrolysis, is indicated as a red diamond sandwiched between the two LptB subunits. Additional cycles of LPS extraction are between steps 4 and 5. See ‘Discussion’ in the main text for description of proposed LPS-extraction cycle. The analyses in f and h were performed once.