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Fig. 4 | BMC Molecular and Cell Biology

Fig. 4

From: ECOD: identification of distant homology among multidomain and transmembrane domain proteins

Fig. 4

Homology between MatE transporter and ABC2 transmembrane domains. Transporters are depicted in cartoon, with the cytoplasm on the bottom and transmembrane region marked by grey boxes. a MatE-like MDR efflux pump (PDB: 3mku) exhibits an internal duplication of two transmembrane bundles (TMs 1–6 and TMs 7–12), with each colored in rainbow from blue to red. A bound monovalent cation (magenta sphere) highlights an outward-facing binding site for molecules of the electrochemical gradient. b The MOP superfamily member MurJ flippase (PDB: 5 t77) adopts a similar overall duplicated topology with a C-terminal two TMH extension to the C-lobe and an inward-facing topology. A sequence motif (magenta) marks a broken TM2 that might contribute to transport. c The ABC2 transmembrane domains from the ABCG5/8 heterodimer (PDB: 5do7) retains a similar overall core topology, except with swapped N-terminal helices. The functional coupling helix (magenta) follows TM2

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