Extended Data Fig. 7: Structural features of MCE domains and ABC transporter transmembrane domains, YrbE1A and YrbE1B.

a, Structural alignment of Mce1 MCE domains colour-coded based on key. Domains were aligned to the MCE domain of Mce1A. Pore-lining loops (PLLs) are circled. b, Protein sequence alignment of the MCE domains from Msmeg Mce1 proteins using MUSCLE⁷⁵ and visualized using JalView⁷⁶. Sequence alignment is coloured by BLOSUM62 score (not conserved, white; conserved, blue). PLL region is highlighted with black bracket and pore facing residues are indicated with black arrows. c, Gallery of Mce1 PPLs. Protein backbones are shown as cartoon tubes with residues shown as sticks and coloured as Extended Data Fig. 7a. Cryo-EM density for the PLLs is shown as a grey transparent surface. Protein densities rendered using ChimeraX⁵³ ‘volume zone’ with 2.0 Å distance cutoff around each PLL at contour level 10.0. Pore facing residues are annotated. d, Topology diagram of YrbE1A, Yrbe1B and E. coli homologue MlaE (derived from PDB 6XBD⁴¹). CH, coupling helix; PH, periplasmic helix; IF, interfacial helix; TM, transmembrane helix. e, Structures of YrbE1A, YrbE1B and MlaE. YrbE1A and YrbE1B form a heterodimer, while MlaE forms a homodimer. One protomer is shown as a cartoon and the other as a molecular surface in each representation. f, View of Mce1 IM complex as indicated by inset on upper left. Model coloured as in the key. The C-terminus of YrbE1B (residues 280–289) is shown as spheres. Grey-dotted lines indicate the MCE ring tilt relative to YrbE1B. g, Zoom-in view of region boxed in Extended Data Fig. 7f, oriented as indicated by inset, highlighting interaction between YrbE1B C-terminus and Mce1F PLL. Proteins are shown as cartoon ribbons and coloured as Extended Data Fig. 7f. Cryo-EM density is shown as a transparent grey surface for the YrbE1B C-terminus (chain J, residues 280–289) and Mce1F PLL (chain F, residues 99–110). Protein densities rendered using ChimeraX⁵³ ‘volume zone’ with 2.0 Å distance cutoff around YrbE1B C-terminus and Mce1F PLL and 8.7 contour level. Hydrogen bonds are shown as cyan dotted lines.