9Z4J

Cryo-EM structure of the mitochondrial NCLX in its trimeric state

Summary for 9Z4J

• Entry DOI: 10.2210/pdb9z4j/pdb
• EMDB information: 73805
• Descriptor: Mitochondrial sodium/calcium exchanger protein, CALCIUM ION, ZINC ION (3 entities in total)
• Functional Keywords: nclx, exchanger, membrane protein
• Biological source: Rattus norvegicus (Norway rat)
• Total number of polymer chains: 3
• Total formula weight: 202332.32

Authors

Zhang, L.,Jiang, Y. (deposition date: 2025-11-10, release date: 2026-07-15, Last modification date: 2026-07-22)

Primary citation

Zhang, L.,Han, Y.,Zeng, W.,Xue, J.,Wang, Y.,Jiang, Y.
Molecular mechanisms of mitochondrial Ca 2+ exchanger NCLX.
Nat Commun, 2026

PubMed Abstract: Mitochondrial Ca²⁺ homeostasis is maintained through coordinated influx and efflux processes, with NCLX long recognized as the primary Ca²⁺ extruder operating via Na⁺/Ca²⁺ exchange. Here, we report cryo-EM structures of rat NCLX in cytosolic-facing occluded and open states. The central transmembrane (TM) domain of NCLX comprises ten helices arranged in two inverted, structurally similar halves, with two α-repeats forming a central ion-binding pocket. Peripheral TMs 1 and 6 are loosely associated with the core and likely mediate alternative access to this site. These structural features closely resemble those of NCXs, indicating a conserved ion exchange mechanism. While NCLX retains the canonical Ca²⁺-binding site, it lacks several key Na⁺-binding residues found in NCXs, suggesting broader ion selectivity. Consistently, cell-based Ca²⁺ uptake assays show that NCLX mediates Ca²⁺ exchange using Na⁺, K⁺, Li⁺, and potentially protons as counterions. Based on the structural symmetry of NCLX and its bidirectional exchange capability, we propose a matrix-facing model and an alternating-access mechanism in which TMs 1 and 6 undergo sliding motions to enable ion exchange between cytosolic and matrix sides, analogous to NCX. These findings provide a structural and mechanistic framework for understanding NCLX-mediated Ca²⁺ transport in mitochondria.

PubMed: 42431881
DOI: 10.1038/s41467-026-75483-x

Experimental method

ELECTRON MICROSCOPY (3.15 Å)