(a) The PR is comprised of N-terminal portions of CagX and a fragment of CagY. Both proteins start from the inner membrane side of the PR, form small globular folds, and extend upward toward the outer membrane. A portion of CagY within the PR wraps around CagX, starting from the periplasm and winding into the lumen of the PR. (b) The N-terminal domain of CagX (residues 41–310) is similar to that of VirB9 (c) from X. citri in both structure and sequence (d). The C-terminal domain of CagX (e) is similar to that of the C-terminal domain of VirB9 from X. citri (f). (g) The periplasmic and outer membrane domains (PD and OMD, respectively) are similar in structurally characterized VirB9 homologs, though they are separated by a periplasmic linker (PL) that is variable in length. CagX contains an additional insertion (residues 102–153, periplasmic insertion or PI) that is unique when compared to other homologs. The structure corresponding to the PI was not observed within any of our cryo-EM reconstructions. (h) The spacing of the two CagX/VirB9 domains varies depending on the organism and appears to be highly dependent on the length of the periplasmic linker (CagX and VirB9 are shown in orange). (i) The segment of CagY within the PR (residues 1469–1603) adopts a highly elongated fold that consists of four α-helices (left). The periplasmic portion of CagY (as shown on the left) starts within the periplasm and wraps around the globular domain of CagX (shown in orange), eventually ending in the lumen of the PR (gray, right). (j) The periplasmic segment of CagY, which we call the periplasmic domain (PD, brown), is unique to CagY and is not present in other VirB10 homologs such as VirB10 from X. citri (yellow indicates a VirB10 like domain, and red represents the unstructured linker). (k) The N-terminus of CagY was not observed within any of these cryo-EM reconstructions. The N-terminal portion of CagY in the model that was constructed (about residue 1469) is positioned so that it might continue outward into the periplasmic space, possibly contributing to the structural feature known as the collar, as well as the stalk.