2.A.19.3.4
Sodium/calcium exchanger 1 (Na⁺/Ca²⁺-exchange protein 1), CNC NCX1 of 973 aas and 12 TMSs in a 6 + 6 TMS arrangement.  The cardiac isoform, CAX1.1, like the archaeal homologues for which high resolution 3-d structures are available (TC#s 2.A.19.5.3 and 2.A.19.8.2), have two aqueous ion permeation channels with cavities that can face the cytoplasm or the external medium (John et al. 2013). It exchanges one Ca²⁺ ion against three to four Na⁺ ions, and thereby contributes to the regulation of cytoplasmic Ca²⁺ levels and Ca²⁺-dependent cellular processes (Komuro et al. 1992; , Van Eylen et al. 2001; Kofuji et al. 1992). It also contributes to Ca²⁺ transport during excitation-contraction coupling in muscle. In a first phase, voltage-gated channels mediate the rapid increase of cytoplasmic Ca²⁺ levels due to release of Ca²⁺ stores from the endoplasmic reticulum. SLC8A1 mediates the export of Ca²⁺ from the cell during the next phase, so that cytoplasmic Ca²⁺ levels rapidly return to baseline. It is also required for normal embryonic heart development and the onset of heart contractions. Both NCX1 and NCX2 play important roles in the motility of the gastric fundus, ileum and distal colon (Nishiyama et al. 2016). An amphipathic α-helix in the NCX1 large intracellular loop controls NCX1 palmitoylation. Thus, NCX1 palmitoylation is governed by a distal secondary structure element rather than by local primary sequence (Plain et al. 2017). The anti-aging gene NM_026333 contributes to proton-induced aging via the NCX1-pathway (Osanai et al. 2018). Dynamic palmitoylation modulates its structure, affinity for lipid-ordered domains, and inhibition by XIP (Gök et al. 2020). Na⁺/Ca²⁺ exchanger, NCX1, and canonical transient receptor potential channel 6 (TRPC6) are recruited by STIM1 to mediate Store-Operated Calcium Entry in primary cortical neurons (Tedeschi et al. 2022). SEA0400 is a potent and selective Na⁺/Ca²⁺ exchanger (NCX) inhibitor (Iwamoto et al. 2004).  Along the proximal tubule and thick ascending limb of the kidney, Ca²⁺ and Na⁺ transport occur in parallel, but those processes were dissociated in the distal convoluted tubule (Hakimi et al. 2023). Xue et al. 2023 presented cryo-EM structures of human cardiac NCX1 in both inactivated and activated states, elucidating key structural elements important for NCX ion exchange and its modulation by cytosolic Ca²⁺ and Na⁺. They showed that the interactions between the ion-transporting transmembrane (TM) domain and the cytosolic regulatory domain define the activity of NCX. In the inward-facing state with low cytosolic [Ca²⁺], a TM-associated four-stranded beta-hub mediates tight packing between the TM and cytosolic domains, resulting in the formation of a stable inactivation assembly that blocks the TM movement required for ion exchange. Ca²⁺ binding to the cytosolic second Ca²⁺-binding domain (CBD2) disrupts this inactivation assembly which releases its constraint on the TM domain, yielding an active exchanger. Thus, the NCX1 structures provide an essential framework for the mechanistic understanding of the ion transport and cellular regulation of NCX family proteins (Xue et al. 2023).  Structural insight into the allosteric inhibition of human sodium-calcium exchanger NCX1 by XIP and SEA0400 have been published (Dong et al. 2024).  The cryo-EM structure of NCX1.3 in the presence of a specific inhibitor, SEA0400 shows that conserved ion-coordinating residues are exposed on the cytoplasmic face of NCX1.3, indicating that the observed structure is stabilized in an inward-facing conformation. The regulatory calcium-binding domains (CBDs) assemble with the ion-translocation transmembrane domain (TMD). The exchanger-inhibitory peptide (XIP) is trapped within a groove between the TMD and CBD2 and is predicted to clash with gating helices TMs(1/6) at the outward-facing state, thus hindering the conformational transition and promoting inactivation of the transporter. A bound SEA0400 molecule stiffens helix TM2ab and affects conformational rearrangements of TM2ab that are associated with the ion-exchange reaction, thus allosterically attenuating Ca²⁺-uptake activity of NCX1.3 (Dong et al. 2024).