Extended Data Fig. 9: A previous PbgA crystal structure reported to have cardiolipin bound at the IFD is, instead, more consistent with bound lipid A.

a, At the inner membrane–periplasmic interface that we term the IFD: cardiolipin (named CL2)⁷ from chain A (left) and chain B (middle) of PDB 6V8Q are shown in stick representation; PbgA is removed for clarity. Similarly, lipid A is shown in stick representation taken from the high-resolution crystal structure presented in this work (right). Molecular clashes calculated using the MOE software⁷⁴ indicate high-energy atomic distance and poor geometry (green lines) in both chains A and B from PDB 6V8Q. The extent of the intramolecular clash is indicated by the relative size of the green circle. b, An F_o − F_c map calculated using coordinates and structure factors from PDB 6V8Q chain A (left) and chain B (middle) shows a strong negative peak (−3σ, red mesh; −4σ, blue mesh) on the assigned modelled P2 phosphate position of the CL2 ligand. Right, the LPS–PbgA complex determined in this work is superimposed onto chain B of PDB 6V8Q for reference, with no further adjustments. c, An F_o − F_c map calculated using coordinates and structure factors from PDB 6V8Q, with CL2 omitted from the calculation, shows strong positive peaks (4σ and 7.5σ for chain A and B, respectively; green mesh), which, in both cases, appear better described by the LPS–PbgA complex structure determined in this work. Shown (right) is the LPS–PbgA complex superimposed onto chain B of PDB 6V8Q with no further adjustments. d, The same F_o − F_c map calculation as in c, only contoured to 3σ (green mesh). As seen on the right, when superimposed onto chain B of 6V8Q, the proximal 1-phospho-GlcNAc group of lipid A in our LPS–PbgA structure appears especially well accounted for by positive density peaks, and density consistent with a KDO sugar head group is also observed; and similar conclusions are reaching upon inspection of superposition onto chain A of 6V8Q (not shown).