Fig. 2: The structure of the NHE transporter module and PA-mediated remodelling.

a, Cryo-EM map of SLC9C1 in GDN detergent with the NHE transporter module circled (left). Middle, cartoon representation of the NHE transporter homodimer, with the dimer domain comprising TM1–TM3 and TM8–TM10 (light orange), and the core domain comprising TM4–TM6 and TM11–TM13 (light yellow). The core and dimer domains are connected by the linker helix TM7 (grey). Right, as described for the middle image, but shown from the extracellular side. b, Cross-section of the electrostatic surface along the side view of the SLC9C1 homodimer in GDN detergent showing the negatively charged inward-facing cavity, the location of the ion-binding site (dotted black circle and purple Na⁺ ion) and the extracellular, hydrophobic gap between protomers with two lipid tails bound (grey sticks). c, As in b, for the SLC9C1 homodimer in nanodiscs, showing the compaction of the extracellular gap and the binding of two PA lipids (grey sticks) and the cryo-EM map density (grey mesh). d, SLC9C1 homodimer in detergent (light orange, dimer domain; yellow, core domain) superimposed with the SLC9C1 homodimer in nanodiscs (grey), showing the compaction of the dimerization interface in the presence of PA lipids (green sticks). e, Electrostatic surface representation of the SLC9C1 monomer and cartoon representation of the half helices TM5a-b and TM12a-b (yellow) and ion-binding site (dotted black circle and purple Na⁺ ion): the crossover half helices are unique to the NhaA-fold and the half-helical dipoles that are formed are denoted (left). Middle, in SLC9C1 Arg431 (green-stick) neutralizes the negatively charged half-helical dipole, and Asp209 (green-stick) neutralizes the positively charged half-helical dipoles. Asn237 and Asp238 in TM6 form the canonical ND motif^15,37, characteristic of electroneutral NHEs. Right, ion-binding site residues for sea urchin SLC9C1 (green sticks) and the corresponding position of ion-binding site residues from horse NHE9 (Protein Data Bank (PDB) 6Z3Z; light blue). In SLC9C1 a salt-bridge (dashed line) is formed between Arg399 in TM11 and Glu233 in TM6.