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Abstract

The Ton and Tol systems are proton‑driven motor complexes that are essential for high‑affinity nutrient uptake and for maintaining outer‑membrane integrity in Gram‑negative bacteria. Their activity depends on coordinated interactions among the inner‑membrane proteins ExbB–ExbD–TonB and TolQ–TolR–TolA, but the structural basis of these interactions has been poorly understood. This paper presents near-atomic-resolution cryo-EM structures of both complexes, revealing a conserved architecture in which a pentameric ExbB or TolQ ring encloses a dimeric ExbD or TolR transmembrane segment.

Overview

Gram-negative bacteria use specialized molecular “motors” in their inner membrane to move energy from the proton motive force (pmf) to the cell surface. The E. coli TolAQR and TonB–ExbBD complexes are two such molecular motors in teh inner membrane that harness the proton motive force (pmf) to drive critical cell envelope processes. Despite acting in parallel pathways with the Tol system maintaining outer membrane integrity and the Ton system powering nutrient import, both complexes share similar architectural design: : pentameric scaffold, embedded proton-linked residues, and a single force-transducing helix (TolA or TonB) that connects the pmf machinery to the cell surface. High-resolution cryo-EM structures shown in this paper reveal how these assemblies are organized and how their subunits couple pmf to mechanical action.

Structure of the E. coli TolAQR Complex

The cryo-EM structure of the TolA–TolQ–TolR complex was obtained after removing the flexible periplasmic portion of TolA which created heterogeneity. This removal was done via a TEV-cleavable construct. The resulting assembly has a 5:2:2 TolQ:TolR:TolA stoichiometry. TolQ forms a pentameric scaffold of seven α-helices per subunit, including three tilted transmembrane helices shaped by conserved proline-induced kinks. TolR forms a dimer within the central hydrophobic pore, with its essential residue Asp23 positioned near a ring of TolQ Thr138/Thr178, creating a proton-linked polar gate. Two TolA transmembrane helices bind peripherally through the conserved SHLS motif, with His22 making key contacts with TolQ. The cytoplasmic domain of TolQ helices are intrinsically flexible showing dynamic nature during pmf driven activities

Structure of the E. coli TonB–ExbBD Complex

The E. coli TonB–ExbBD complex is a 1:5:2 assembly in which five ExbB subunits form a tilted-helix pentameric scaffold that encloses a parallel but axially offset dimer of ExbD transmembrane helices. The ExbB pentamer generates a hydrophobic central pore into which the ExbD TM dimer inserts, while the N-terminal cytoplasmic domains of ExbD form an asymmetric pair stabilized by conserved ExbB residues. The TonB forms a single transmembrane helix with a conserved SHLS motif. The transmembrane helix is tilted ~15° in the membrane and interacts with the ExbB through conserved TonB Ser16 and His20. The complex also contains tightly bound phosphatidylethanolamine lipids at ExbB subunit interfaces.

References

Celia, H., Botos, I., Ghirlando, R., Duché, D., Beach, B. M., Lloubes, R., & Buchanan, S. K. (2025). Cryo-EM structures of the E. coli Ton and Tol motor complexes. Nature Communications, 16, 5506. [1](https://doi.org/10.1038/s41467-025-61286-z)

About this Page

This page was created by Niranjana Vinod.
University/Institution Name (Indian Institute of Science Education and Research,Pune)