Structures of the β-barrel assembly machine recognizing outer membrane protein substrates

beta-barrel outer membrane proteins (beta-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of beta-OMPs in Gram-negative bacteria is mediated by the beta-barrel assembly machinery (BAM) complex, yet its precise mechanism remains elusive. Here, we report two structures of the BAM complex in detergents and in nanodisks, and two crystal structures of the BAM complex with bound substrates. Structural analysis indicates that the membrane compositions surrounding the BAM complex could modulate its overall conformations, indicating low energy barriers between different conformational states and a highly dynamic nature of the BAM complex. Importantly, structures of the BAM complex with bound substrates and the related functional analysis show that the first beta-strand of the BamA beta-barrel (beta 1(BamA)) in the BAM complex is associated with the last but not the first beta-strand of a beta-OMP substrate via antiparallel beta-strand interactions. These observations are consistent with the beta-signal hypothesis during beta-OMP biogenesis, and suggest that the beta 1(BamA) strand in the BAM complex may interact with the last beta-strand of an incoming beta-OMP substrate upon their release from the chaperone-bound state.