a, Atomic representation of an O1 O-antigen ligation to the R1 lipid A core oligosaccharide. The O-antigen is transferred to the lipid A core oligosaccharide by WaaL, forming the mature LPS. After ligation, Und-PP is recycled. b, Cryo-EM density map of the Und-PP-bound CmWaaL–Fab complex. Density corresponding to the variable region of the Fab (vFAB) is shown in grey and CmWaaL in rainbow colour. Representation is in rainbow colour from the N terminus (blue) to the C terminus (red). c, Schematic diagram showing the topology of WaaL, consisting of 12 TM helices and a large periplasmic loop between TM9 and TM10. d, The 3.2 Å cryo-EM structure of Und-PP-bound WaaL shown in two different orientations, with the 12 TM helices coloured as in c. The N and C termini are labelled. The right-hand side shows a 90° rotation with helices numbered, as viewed from the top. Und-PP is shown as sticks (in gold). Approximate membrane boundaries are represented with dotted lines.