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- PDB-9z4j: Cryo-EM structure of the mitochondrial NCLX in its trimeric state -

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Basic information

Entry
Database: PDB / ID: 9z4j
TitleCryo-EM structure of the mitochondrial NCLX in its trimeric state
ComponentsMitochondrial sodium/calcium exchanger protein
KeywordsMEMBRANE PROTEIN / NCLX / exchanger
Function / homology
Function and homology information


calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of lymphocyte chemotaxis / Mitochondrial calcium ion transport / Sodium/Calcium exchangers / calcium export from the mitochondrion / calcium:sodium antiporter activity / mitochondrial calcium ion transmembrane transport / regulation of cardiac muscle cell membrane potential / mitochondrial calcium ion homeostasis / regulation of store-operated calcium entry ...calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of lymphocyte chemotaxis / Mitochondrial calcium ion transport / Sodium/Calcium exchangers / calcium export from the mitochondrion / calcium:sodium antiporter activity / mitochondrial calcium ion transmembrane transport / regulation of cardiac muscle cell membrane potential / mitochondrial calcium ion homeostasis / regulation of store-operated calcium entry / mitochondrial crista / regulation of insulin secretion / regulation of cytosolic calcium ion concentration / sodium ion transmembrane transport / sarcolemma / mitochondrial membrane / intracellular calcium ion homeostasis / calcium ion transmembrane transport / glucose homeostasis / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein
Similarity search - Domain/homology
Mitochondrial sodium/calcium exchanger protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhang, L. / Jiang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140892 United States
CitationJournal: To Be Published
Title: Molecular mechanisms of mitochondrial Na+/ Ca2+ exchanger NCLX
Authors: Zhang, L. / Jiang, Y.
History
DepositionNov 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mitochondrial sodium/calcium exchanger protein
B: Mitochondrial sodium/calcium exchanger protein
C: Mitochondrial sodium/calcium exchanger protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,3327
Polymers202,1473
Non-polymers1864
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Mitochondrial sodium/calcium exchanger protein / Na(+)/K(+)/Ca(2+)-exchange protein 6 / Sodium/calcium exchanger protein / mitochondrial / ...Na(+)/K(+)/Ca(2+)-exchange protein 6 / Sodium/calcium exchanger protein / mitochondrial / Sodium/potassium/calcium exchanger 6 / Solute carrier family 24 member 6 / Solute carrier family 8 member B1


Mass: 67382.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc8b1, Nckx6, Nclx, Slc24a6 / Production host: Homo sapiens (human) / References: UniProt: Q6AXS0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial sodium/calcium exchanger in complex with calcium
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
EM software
IDNameVersionCategory
1RELION5particle selection
4RELION5CTF correction
7RELION5model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47504 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingDetails: The initial model used here is ab initio model / Source name: Other / Type: in silico model
RefinementHighest resolution: 3.15 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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