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- EMDB-60921: Cryo-EM structure of human NCX1 in PIP2 diC8 bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-60921
TitleCryo-EM structure of human NCX1 in PIP2 diC8 bound state
Map data
Sample
  • Complex: human cardiac sodium calcium exchanger NCX1
    • Protein or peptide: Sodium/calcium exchanger 1
  • Ligand: CALCIUM ION
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
Keywordssodium calcium exchanger / Na/Ca exchanger / TRANSPORT PROTEIN
Function / homology
Function and homology information


relaxation of smooth muscle / calcium:sodium antiporter activity / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / membrane depolarization during cardiac muscle cell action potential / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / regulation of the force of heart contraction / negative regulation of protein serine/threonine kinase activity ...relaxation of smooth muscle / calcium:sodium antiporter activity / vascular associated smooth muscle contraction / calcium ion export / regulation of cell communication by electrical coupling / membrane depolarization during cardiac muscle cell action potential / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / regulation of the force of heart contraction / negative regulation of protein serine/threonine kinase activity / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / calcium ion import / regulation of cardiac muscle contraction by calcium ion signaling / calcium ion transport into cytosol / Sodium/Calcium exchangers / cardiac muscle cell development / Reduction of cytosolic Ca++ levels / relaxation of cardiac muscle / ankyrin binding / calcium ion transmembrane import into cytosol / negative regulation of cytosolic calcium ion concentration / positive regulation of the force of heart contraction / cellular response to caffeine / calcium ion import across plasma membrane / intercalated disc / regulation of cardiac conduction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of bone mineralization / calcium ion homeostasis / monoatomic ion transport / cardiac muscle contraction / Ion homeostasis / cytoskeletal protein binding / muscle contraction / T-tubule / axon terminus / response to muscle stretch / sodium ion transmembrane transport / 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 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily ...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 / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein / CalX-like domain superfamily / DnaJ domain
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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
CitationJournal: To Be Published
Title: Structural mechanisms of human cardiac sodium calcium exchanger NCX1
Authors: Xue J / Jiang Y
History
DepositionJul 23, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60921.png

Downloads & links

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Map

FileDownload / File: emd_60921.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.6003635 - 4.1552997
Average (Standard dev.)0.0015911028 (±0.06296779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_60921_additional_1.map
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Additional map: #1

Fileemd_60921_additional_2.map
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Half map: #2

Fileemd_60921_half_map_1.map
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Half map: #1

Fileemd_60921_half_map_2.map
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Sample components

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Entire : human cardiac sodium calcium exchanger NCX1

EntireName: human cardiac sodium calcium exchanger NCX1
Components
  • Complex: human cardiac sodium calcium exchanger NCX1
    • Protein or peptide: Sodium/calcium exchanger 1
  • Ligand: CALCIUM ION
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Supramolecule #1: human cardiac sodium calcium exchanger NCX1

SupramoleculeName: human cardiac sodium calcium exchanger NCX1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 3 / Number of copies: 1 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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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

MicroscopeFEI TECNAI SPHERA
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: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117748
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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