Fig. 1: The periplasmic domain of ExbD forms a homodimer.
From: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake
a The Ton system consists of an inner membrane proton channel – formed by ExbB (grey) and ExbD (pink) – and the periplasm spanning protein TonB (blue). The latter links the system to a TonB-dependent transporter in the outer membrane. The globular C-terminal domain of ExbD (pink boxes) is connected to its helical N-terminus, which is inserted into the ExbB channel, by a disordered region (pink, wiggly lines). b Sedimentation coefficient distribution obtained from analytical ultracentrifugation of ExbDSm, peri and ExbDEc, peri indicates that both proteins exist in a dimeric state at physiological pH. The red dashed lines represent estimated sedimentation coefficients for monomeric ExbD and dimeric ExbD as depicted by the cartoons (pink). The sedimentation coefficient-derived molecular weights of both species are indicated above. c The top view of the NMR structure ensemble of dimeric ExbDSm, peri reveals that the N-terminal residues 44–49 (green) form an intermolecular β-sheet. d Homodimeric ExbDSm, peri consists of two monomers (pink and light pink), each with a β-sheet (arrows) and two α-helices (barrels). Part of the dimeric interface is formed by a swapped, intermolecular, and anti-parallel β-sheet called the N-terminal Intermolecular Beta-Strand (NIBS, green). The NIBS, composed of residues 44-49, connects the intramolecular β-sheets, creating a continuous β-sheet across the dimer interface. In the full-length protein, ExbDSm, peri is N-terminally connected to two α-helices (α1) that are embedded in the ExbB channel (grey). e Side view and f Top view of the AlphaFold2 model of the full ExbB-ExbD complex, generated using the NMR structure (PDB ID 8PEK structure of the dimeric, periplasmic domain of ExbD, this work) as a template. In this model, the dimeric organization of the periplasmic domain of ExbD (pink and light pink) imposes the alignment of its helices in similar positions and orientations, and locking both Asp 25 sidechains in hydrogen bonds with Thr 218 from ExbB. In the top view, the periplasmic domain of ExbD is not visible due to its location above the clipping plane. Source data are provided as a Source Data file.
