Structural basis of gate dynamics at the outer membrane lipopolysaccharide holo-translocon

Gram-negative bacteria resist many harmful chemicals, protected by an asymmetric outer membrane (OM) containing lipopolysaccharide (LPS) in its external leaflet. Leaflet-selective assembly of LPS is an essential, yet mechanistically elusive process. This reaction is mediated by the OM LPS core translocon, composed of the transmembrane protein LptD and its cognate lipoprotein LptE. Here, we characterize two additional translocon subunits, the lipoproteins LptM and YedD, uncovering their impact on LptD conformational dynamics. This dataset includes native MS allowing the identification of YedD, after gas-phase dissociation from the LptDE/LptDEM complexes (complex-down MS). We also include here bottom-up proteomics data after trypsin digestion from SDS-PAGE gel bands, confirming the nature of YedD in the purified complex.