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- EMDB-40456: Cryo-EM structure of human NCX1 in complex with SEA0400 -

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Basic information

Entry
Database: EMDB / ID: EMD-40456
TitleCryo-EM structure of human NCX1 in complex with SEA0400
Map data
Sample
  • Complex: human NCX1-SEA0400 in complex with antibody Fab fragment
    • Complex: human cardiac sodium calcium exchanger NCX1 in complex with SEA0400
      • Protein or peptide: Sodium/calcium exchanger 1
    • Complex: antibody Fab fragment
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
  • Ligand: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsNa/Ca exchanger / sodium calcium exchanger / TRANSPORT PROTEIN
Function / homology
Function and homology information


relaxation of smooth muscle / negative regulation of intracellular signal transduction / vascular associated smooth muscle contraction / calcium:sodium antiporter activity / regulation of cell communication by electrical coupling / calcium ion export / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction ...relaxation of smooth muscle / negative regulation of intracellular signal transduction / vascular associated smooth muscle contraction / calcium:sodium antiporter activity / regulation of cell communication by electrical coupling / calcium ion export / membrane depolarization during cardiac muscle cell action potential / regulation of the force of heart contraction / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / calcium ion import / calcium ion transport into cytosol / relaxation of cardiac muscle / cardiac muscle cell development / regulation of cardiac muscle contraction by calcium ion signaling / Sodium/Calcium exchangers / ankyrin binding / Reduction of cytosolic Ca++ levels / cellular response to caffeine / calcium ion transmembrane import into cytosol / negative regulation of cytosolic calcium ion concentration / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / intercalated disc / regulation of cardiac conduction / positive regulation of bone mineralization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / cytoskeletal protein binding / cardiac muscle contraction / Ion homeostasis / monoatomic ion transport / response to muscle stretch / axon terminus / T-tubule / sodium ion transmembrane transport / muscle contraction / regulation of heart rate / cell periphery / cellular response to reactive oxygen species / sarcolemma / calcium ion transmembrane transport / Z disc / intracellular calcium ion homeostasis / regulation of gene expression / transmembrane transporter binding / calmodulin binding / postsynapse / postsynaptic density / axon / neuronal cell body / dendrite / calcium ion binding / synapse / nucleoplasm / plasma membrane
Similarity search - Function
Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region ...Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / : / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / DnaJ domain
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXue J / Jiang Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140892 United States
Welch FoundationI-1578 United States
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Elife / Year: 2025
Title: Structural mechanisms of PIP 2 activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1.
Authors: Xue J / Zeng W / John S / Attiq N / Ottolia M / Jiang Y
#1: Journal: Biorxiv / Year: 2025
Title: Structural mechanisms of PIP 2 activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1.
Authors: Xue J / Zeng W / John S / Attiq N / Ottolia M / Jiang Y
History
DepositionApr 12, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40456.png

Downloads & links

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Map

FileDownload / File: emd_40456.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.51
Minimum - Maximum-2.6429603 - 4.1449957
Average (Standard dev.)0.0022546155 (±0.070893034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused TM map2 of NCX1 in complex with SEA0400

Fileemd_40456_additional_1.map
Annotationfocused TM map2 of NCX1 in complex with SEA0400
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused TM map1 of NCX1 in complex with SEA0400

Fileemd_40456_additional_2.map
Annotationfocused TM map1 of NCX1 in complex with SEA0400
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused CBD map of NCX1 in complex with SEA0400

Fileemd_40456_additional_3.map
Annotationfocused CBD map of NCX1 in complex with SEA0400
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40456_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_40456_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 : human NCX1-SEA0400 in complex with antibody Fab fragment

EntireName: human NCX1-SEA0400 in complex with antibody Fab fragment
Components
  • Complex: human NCX1-SEA0400 in complex with antibody Fab fragment
    • Complex: human cardiac sodium calcium exchanger NCX1 in complex with SEA0400
      • Protein or peptide: Sodium/calcium exchanger 1
    • Complex: antibody Fab fragment
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
  • Ligand: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline
  • Ligand: CALCIUM ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: human NCX1-SEA0400 in complex with antibody Fab fragment

SupramoleculeName: human NCX1-SEA0400 in complex with antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: human cardiac sodium calcium exchanger NCX1 in complex with SEA0400

SupramoleculeName: human cardiac sodium calcium exchanger NCX1 in complex with SEA0400
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: antibody Fab fragment

SupramoleculeName: antibody Fab fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Sodium/calcium exchanger 1

MacromoleculeName: Sodium/calcium exchanger 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.18107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYNMRRLSLS PTFSMGFHLL VTVSLLFSHV DHVIAETEME GEGNETGECT GSYYCKKGVI LPIWEPQDPS FGDKIARATV YFVAMVYMF LGVSIIADRF MSSIEVITSQ EKEITIKKPN GETTKTTVRI WNETVSNLTL MALGSSAPEI LLSVIEVCGH N FTAGDLGP ...String:
MYNMRRLSLS PTFSMGFHLL VTVSLLFSHV DHVIAETEME GEGNETGECT GSYYCKKGVI LPIWEPQDPS FGDKIARATV YFVAMVYMF LGVSIIADRF MSSIEVITSQ EKEITIKKPN GETTKTTVRI WNETVSNLTL MALGSSAPEI LLSVIEVCGH N FTAGDLGP STIVGSAAFN MFIIIALCVY VVPDGETRKI KHLRVFFVTA AWSIFAYTWL YIILSVISPG VVEVWEGLLT FF FFPICVV FAWVADRRLL FYKYVYKRYR AGKQRGMIIE HEGDRPSSKT EIEMDGKVVN SHVENFLDGA LVLEVDERDQ DDE EARREM ARILKELKQK HPDKEIEQLI ELANYQVLSQ QQKSRAFYRI QATRLMTGAT ENDPVSKIFF EQGTYQCLEN CGTV ALTII RRGGDLTNTV FVDFRTEDGT ANAGSDYEFT EGTVVFKPGD TQKEIRVGII DDDIFEEDEN FLVHLSNVKV SSEAS EDGI LEANHVSTLA CLGSPSTATV TIFDDDHAGI FTFEEPVTHV SESIGIMEVK VLRTSGARGN VIVPYKTIEG TARGGG EDF EDTCGELEFQ NDEIVKTISV KVIDDEEYEK NKTFFLEIGE PRLVEMSEKK ALLLNELGGF TITGKYLFGQ PVFRKVH AR EHPILSTVIT IADEYDDKQP LTSKEEEERR IAEMGRPILG EHTKLEVIIE ESYEFKSTVD KLIKKTNLAL VVGTNSWR E QFIEAITVSA GEDDDDDECG EEKLPSCFDY VMHFLTVFWK VLFAFVPPTE YWNGWACFIV SILMIGLLTA FIGDLASHF GCTIGLKDSV TAVVFVALGT SVPDTFASKV AATQDQYADA SIGNVTGSNA VNVFLGIGVA WSIAAIYHAA NGEQFKVSPG TLAFSVTLF TIFAFINVGV LLYRRRPEIG GELGGPRTAK LLTSCLFVLL WLLYIFFSSL EAYCHIKGFA AAGGSWSHPQ F EKGGGSGG GSGGSAWSHP QFEK

UniProtKB: Sodium/calcium exchanger 1

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Macromolecule #2: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.740082 KDa
SequenceString: QAVVTQESAL TTSPGETVTL TCRSSTGAVT TSNYANWVQE KPDHLFTGLI GGTNNRVPGV PARFSGSLIG DKAALTITGA QTEDEAIYF CALWYSNHWV FGGGTKLTVL GQPKSSPSVT LFPPSSEELE TNKATLVCTI TDFYPGVVTV DWKVDGTPVT Q GMETTQPS ...String:
QAVVTQESAL TTSPGETVTL TCRSSTGAVT TSNYANWVQE KPDHLFTGLI GGTNNRVPGV PARFSGSLIG DKAALTITGA QTEDEAIYF CALWYSNHWV FGGGTKLTVL GQPKSSPSVT LFPPSSEELE TNKATLVCTI TDFYPGVVTV DWKVDGTPVT Q GMETTQPS KQSNNKYMAS SYLTLTARAW ERHSSYSCQV THEG

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Macromolecule #3: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.435598 KDa
SequenceString: QVQLQQSGAE LARPGASVKL SCKATGYSFT SYWMQWVKQR PGQGMEWIGA IYPGDVTSRY TQKFKGKATL TADKSSSTAF MQLRSLASE DSAVYYCARW SGYYGSSSFD YWGQGTTLTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS ...String:
QVQLQQSGAE LARPGASVKL SCKATGYSFT SYWMQWVKQR PGQGMEWIGA IYPGDVTSRY TQKFKGKATL TADKSSSTAF MQLRSLASE DSAVYYCARW SGYYGSSSFD YWGQGTTLTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS SSVHTFPALL QSGLYTMSSS VTVPSSTWPS QTVTCSVAHP ASSTTVDKKL EPSGPISTIN PCPPCKECHK CP APNLEGG PS

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Macromolecule #4: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline

MacromoleculeName: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline
type: ligand / ID: 4 / Number of copies: 1 / Formula: EKY
Molecular weightTheoretical: 371.377 Da
Chemical component information

ChemComp-EKY:
2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 368227
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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