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- EMDB-71826: Cryo-EM structure of NCLX with calcium (class 2a) -

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Basic information

Entry
Database: EMDB / ID: EMD-71826
TitleCryo-EM structure of NCLX with calcium (class 2a)
Map data
Sample
  • Complex: NCLX without Calcium
    • Protein or peptide: NCLX
  • Ligand: CALCIUM ION
KeywordsMembrane transporter / MEMBRANE PROTEIN
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 speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhang J / Feng L
Funding support United States, 2 items
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 25, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71826.png

Downloads & links

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Map

FileDownload / File: emd_71826.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.001923369 - 1.8542001
Average (Standard dev.)0.0016780292 (±0.030662354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71826_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_71826_half_map_1.map
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Half map: #1

Fileemd_71826_half_map_2.map
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Sample components

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Entire : NCLX without Calcium

EntireName: NCLX without Calcium
Components
  • Complex: NCLX without Calcium
    • Protein or peptide: NCLX
  • Ligand: CALCIUM ION

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Supramolecule #1: NCLX without Calcium

SupramoleculeName: NCLX without Calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NCLX

MacromoleculeName: NCLX / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 64.037688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGRWLDPLW APGFLCVALI LETASGAGDL STKAHGHIQF SARGVNQTAM ADCRAVCSLN TSDRCDFVKR NPDCHSEGGY LDYLKGIFC YFPPNLLPLA ITLYVFWLLY LFLILGVTAA KFFCPNLSAI STSLKLSHNV AGVTFLAFGN GAPDIFSALV A FSDPRTAG ...String:
MAGRWLDPLW APGFLCVALI LETASGAGDL STKAHGHIQF SARGVNQTAM ADCRAVCSLN TSDRCDFVKR NPDCHSEGGY LDYLKGIFC YFPPNLLPLA ITLYVFWLLY LFLILGVTAA KFFCPNLSAI STSLKLSHNV AGVTFLAFGN GAPDIFSALV A FSDPRTAG LAIGALFGAG VLVTTVVAGG ITILRPFMAA SRPFLRDITF YMVAVFLTFT ALYLGRITLV WALGYLGLYV FY VVTVIIC TWVYQRQRSR SLVHSISETP ELLTDSEEDQ MSSNTNSYDY GEEYRPLLLG EETTGQILLQ ALNPLDYRKW RTQ SISCKL LKVAKLPVEF LLLLTVPVVD PDKDDRNWKR PLNCLQLVIS PLVLVLTLQS GVYGIYEIGG LLPVWAVVVI VGTA LASVT FFATSNSEPP RLHWLFAFLG FLTSALWINA AATEVVNILR SLGVVFRLSN TVLGLTLLAW GNSIGDAFSD FTLAR QGYP RMAFSACFGG IIFNILVGVG LGCLLQIVRS HASEVKLEPD GLLVWVLASA LGLSLVFSLV SVPLQCFQLS KAYGLC LLL FYICFIVVVL LTEFGVIHLK AD

UniProtKB: Mitochondrial sodium/calcium exchanger protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 145777
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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