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- EMDB-73804: Cryo-EM structure of the mitochondrial NCLX in its monomeric state -

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Basic information

Entry
Database: EMDB / ID: EMD-73804
TitleCryo-EM structure of the mitochondrial NCLX in its monomeric state
Map data
Sample
  • Complex: mitochondrial sodium/calcium exchanger in complex with calcium
    • Protein or peptide: Mitochondrial sodium/calcium exchanger protein
  • Ligand: SODIUM ION
KeywordsNCLX / exchanger / 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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsZhang L / Jiang Y
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73804.png

Downloads & links

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Map

FileDownload / File: emd_73804.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 288 pix.
= 213.984 Å		0.74 Å/pix.
x 288 pix.
= 213.984 Å		0.74 Å/pix.
x 288 pix.
= 213.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.09476112 - 0.13876358
Average (Standard dev.)-0.0000037927812 (±0.004024253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 213.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73804_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73804_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mitochondrial sodium/calcium exchanger in complex with calcium

EntireName: mitochondrial sodium/calcium exchanger in complex with calcium
Components
  • Complex: mitochondrial sodium/calcium exchanger in complex with calcium
    • Protein or peptide: Mitochondrial sodium/calcium exchanger protein
  • Ligand: SODIUM ION

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Supramolecule #1: mitochondrial sodium/calcium exchanger in complex with calcium

SupramoleculeName: mitochondrial sodium/calcium exchanger in complex with calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Mitochondrial sodium/calcium exchanger protein

MacromoleculeName: Mitochondrial sodium/calcium exchanger protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 67.382227 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 ADAAAGGSWS HPQFEKGGGS GGGSGGGSAW SHPQFEK

UniProtKB: Mitochondrial sodium/calcium exchanger protein

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 1
Molecular weightTheoretical: 22.99 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 IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 336224
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: The initial model used here is the ab initial model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9z4i:
Cryo-EM structure of the mitochondrial NCLX in its monomeric state

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