The function of the β-Barrel Assembly Machinery (BAM) located at the outer membrane (OM) of Gram-negative bacteria is to fold and insert integral membrane proteins into the OM. BAM is a five-member protein complex consisting of BamA, an integral membrane protein itself, and four lipoproteins BamB, C, D, and E. The structures of the components of BAM have been determined; but the overall architecture of the machine remains elusive. BamA is the central component of the machine and interacts with BamB, as well as with BamCDE subcomplex. BamA consists of a C-terminal membrane domain and an N-terminal domain, known as Polypeptide Transport Associated (POTRA) domain. There are five POTRA domains at the N-terminus of BamA. Here we report a structure of a complex between BamB and fragment of BamA’s periplasmic domain refined to a 3.3 Å resolution. The structure was determined from a soluble chimeric protein made of POTRA3-5 of BamA at the N-terminus attached with a 12 amino acid residue linker to BamB at the C-terminus. The interface of BamA-BamB is stabilized by a network of hydrogen bonds and a cation-π interaction in the center. BamB residue R195 was previously shown to abolish BamA-BamB interaction. In our structure, the residue is located in the conserved BamB loop and forms a cation-π interaction with Y255 located in the middle of β3-strand of POTRA3 on BamA. Our structure contradicts a previous suggestion that β2-strand of POTRA3 may bind BamB through β-augmentation. Our structure and complementary mutagenesis studies show that BamB interacts with BamA at the face of the POTRA3 β-sheet, close to its connection to POTRA2. This is consistent with the hypothesis that BamB modulates hinge motions between POTRA2 and 3 of BamA that occur during OM protein folding and/or insertion.