9RHE
Cryo-EM structure of the inward-facing apo NhaA with flexible N-terminus at pH 8.5
Summary for 9RHE
| Entry DOI | 10.2210/pdb9rhe/pdb |
| Related | 9RH1 |
| EMDB information | 53967 |
| Descriptor | Na(+)/H(+) antiporter NhaA, Fv6F9 heavy chain, Fv6F9 light chain (3 entities in total) |
| Functional Keywords | nhaa, sodium proton exchanger, transport protein |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 3 |
| Total formula weight | 70713.83 |
| Authors | Weng, T.-H.,Safarian, S.,Michel, H. (deposition date: 2025-06-08, release date: 2026-06-17, Last modification date: 2026-07-01) |
| Primary citation | Weng, T.H.,Fabian, B.,Olkhova, E.,Welsch, S.,Schmidt, S.L.,Danieli, T.,Keren, Y.,Rimon, A.,Safarian, S.,Hummer, G.,Padan, E.,Michel, H. pH-dependent activation of the Na + /H + antiporter NhaA and conformational dynamics of its N-terminus. Nat Commun, 2026 Cited by PubMed Abstract: Na⁺/H⁺ antiporters are vital for regulating intracellular pH and sodium ion levels across all domains of life. In Escherichia coli, NhaA is the principal Na⁺/H⁺ antiporter, exhibiting strong pH sensitivity and rapid turnover, yet the structural transitions underlying its activation and substrate recognition have remained obscure. Here, we use single-particle cryo-electron microscopy to determine the conformational ensemble of NhaA across a physiological pH range and in the presence of Na⁺, complemented by constant-pH molecular dynamics simulations. High-resolution structures of apo and Na⁺-bound NhaA reconstituted in lipid nanodiscs reveal progressive opening of the cytoplasmic funnel with increasing pH. We also visualize the previously unresolved N-terminal tail, which forms a dynamic plug at the cytoplasmic entrance under low-pH conditions and disengages at alkaline pH, coinciding with activation. The Na⁺-bound structure captures Na⁺ coordination at the ion-binding site, and simulations suggest potential roles for the conserved charged residues. Together, these findings illuminate how pH sensing, N-terminal gating, and substrate binding are structurally coordinated in NhaA, providing a framework for understanding Na⁺/H⁺ antiporter activation and regulation, and the basis for targeting clinical important antiporters. PubMed: 42285937DOI: 10.1038/s41467-026-73424-2 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.5 Å) |
Structure validation
Download full validation report
