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- PDB-9ps1: Cryo-EM structure of NCLX with calcium (class 3a) -

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Basic information

Entry
Database: PDB / ID: 9ps1
TitleCryo-EM structure of NCLX with calcium (class 3a)
ComponentsNCLX
KeywordsMEMBRANE PROTEIN / Membrane transporter
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 cytosolic calcium ion concentration / regulation of insulin secretion / sodium ion transmembrane transport / sarcolemma / mitochondrial membrane / calcium ion transmembrane transport / intracellular calcium ion homeostasis / glucose homeostasis / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / identical protein binding / membrane / 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: 2.6 Å
AuthorsZhang, J. / Feng, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
The G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Nature / Year: 2025
Title: Structure and mechanism of the mitochondrial calcium transporter NCLX.
Authors: Minrui Fan / Chen-Wei Tsai / Jinru Zhang / Jianxiu Zhang / Aswini R Krishnan / Tsung-Yun Liu / Yu-Lun Huang / Deniz Aydin / Siyuan Du / Briana L Sobecks / Madison X Rodriguez / Andrew H ...Authors: Minrui Fan / Chen-Wei Tsai / Jinru Zhang / Jianxiu Zhang / Aswini R Krishnan / Tsung-Yun Liu / Yu-Lun Huang / Deniz Aydin / Siyuan Du / Briana L Sobecks / Madison X Rodriguez / Andrew H Reiter / Carolyn R Bertozzi / Ron O Dror / Ming-Feng Tsai / Liang Feng /
Abstract: As a key mitochondrial Ca transporter, NCLX regulates intracellular Ca signalling and vital mitochondrial processes. The importance of NCLX in cardiac and nervous-system physiology is reflected by ...As a key mitochondrial Ca transporter, NCLX regulates intracellular Ca signalling and vital mitochondrial processes. The importance of NCLX in cardiac and nervous-system physiology is reflected by acute heart failure and neurodegenerative disorders caused by its malfunction. Despite substantial advances in the field, the transport mechanisms of NCLX remain unclear. Here we report the cryo-electron microscopy structures of NCLX, revealing its architecture, assembly, major conformational states and a previously undescribed mechanism for alternating access. Functional analyses further reveal an unexpected transport function of NCLX as a H/Ca exchanger, rather than as a Na/Ca exchanger as widely believed. These findings provide critical insights into mitochondrial Ca homeostasis and signalling, offering clues for developing therapies to treat diseases related to abnormal mitochondrial Ca.
History
DepositionJul 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NCLX
C: NCLX
A: NCLX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,2336
Polymers192,1133
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein NCLX / Mitochondrial sodium/calcium exchanger protein / Na(+)/K(+)/Ca(2+)-exchange protein 6 / ...Mitochondrial sodium/calcium exchanger protein / 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: 64037.688 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 / Feature type: SUBJECT OF INVESTIGATION
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: NCLX without Calcium / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Rattus norvegicus (Norway rat)10116
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: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1Topazparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150233 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00911610
ELECTRON MICROSCOPYf_angle_d0.80715870
ELECTRON MICROSCOPYf_dihedral_angle_d4.8361566
ELECTRON MICROSCOPYf_chiral_restr0.0511932
ELECTRON MICROSCOPYf_plane_restr0.0071929

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