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- EMDB-54118: Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obta... -

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Basic information

Entry
Database: EMDB / ID: EMD-54118
TitleHuman alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obtained under turnover conditions
Map datamain map, 3SD
Sample
  • Complex: Human Na,K-ATPase alpha3/beta1/FXYD1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Phospholemman
  • Ligand: CHOLESTEROL
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHITE ION
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsactive ion transport / P-type ATPase / Na/K-ATPase / E1P / MEMBRANE PROTEIN / METAL TRANSPORT
Function / homology
Function and homology information


negative regulation of protein glutathionylation / protein transport into plasma membrane raft / neuron to neuron synapse / Na+/K+-exchanging ATPase / regulation of cardiac muscle cell membrane potential / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of resting membrane potential / photoreceptor inner segment membrane / steroid hormone binding ...negative regulation of protein glutathionylation / protein transport into plasma membrane raft / neuron to neuron synapse / Na+/K+-exchanging ATPase / regulation of cardiac muscle cell membrane potential / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of resting membrane potential / photoreceptor inner segment membrane / steroid hormone binding / membrane repolarization during cardiac muscle cell action potential / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / regulation of calcium ion transmembrane transport / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / intracellular sodium ion homeostasis / response to glycoside / relaxation of cardiac muscle / regulation of heart contraction / regulation of cardiac muscle contraction by calcium ion signaling / chloride transport / Basigin interactions / cellular response to steroid hormone stimulus / chloride channel activity / ATPase activator activity / neuronal cell body membrane / organelle membrane / intracellular potassium ion homeostasis / potassium ion import across plasma membrane / Ion transport by P-type ATPases / intercalated disc / lateral plasma membrane / sodium channel regulator activity / transporter activator activity / sperm flagellum / ATP metabolic process / cardiac muscle contraction / Ion homeostasis / neuron projection maintenance / photoreceptor inner segment / muscle contraction / proton transmembrane transport / T-tubule / protein localization to plasma membrane / sodium ion transmembrane transport / sarcolemma / caveola / intracellular calcium ion homeostasis / cellular response to amyloid-beta / regulation of gene expression / MHC class II protein complex binding / amyloid-beta binding / extracellular vesicle / ATPase binding / protein-folding chaperone binding / response to hypoxia / Potential therapeutics for SARS / basolateral plasma membrane / transmembrane transporter binding / protein-macromolecule adaptor activity / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / innate immune response / axon / neuronal cell body / synapse / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium and potassium ATPases beta subunits signature 2. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Phospholemman / Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-transporting ATPase subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChristensen ME / Habeck M / Katz A / Fruergaard MU / Karlish SJD / Nissen P
Funding supportEuropean Union, Denmark, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission793086European Union
LundbeckfondenR310-2018-3713 Denmark
Novo Nordisk FoundationNNF20OC0060483 Denmark
The Carlsberg FoundationCF22-1535 Denmark
The Carlsberg FoundationCF23-1394 Denmark
CitationJournal: Nat Commun / Year: 2026
Title: Active conformations of neuronal Na+, K+-ATPase isoforms and a disease-causing mutant
Authors: Christensen ME / Habeck M / Katz A / Fruergaard MU / Peleg Y / Pick U / Karlish SJD / Nissen P
History
DepositionJun 20, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54118.png

Downloads & links

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Map

FileDownload / File: emd_54118.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map, 3SD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 200 pix.
= 248.44 Å		1.24 Å/pix.
x 200 pix.
= 248.44 Å		1.24 Å/pix.
x 200 pix.
= 248.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0678
Minimum - Maximum-0.3498555 - 0.74042195
Average (Standard dev.)0.00020440771 (±0.022602713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 248.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharp map, 3SD

Fileemd_54118_additional_1.map
AnnotationSharp map, 3SD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half A, 3SD

Fileemd_54118_half_map_1.map
Annotationmap half A, 3SD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half B, 3SD

Fileemd_54118_half_map_2.map
Annotationmap half B, 3SD
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 Na,K-ATPase alpha3/beta1/FXYD1

EntireName: Human Na,K-ATPase alpha3/beta1/FXYD1
Components
  • Complex: Human Na,K-ATPase alpha3/beta1/FXYD1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-3
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Phospholemman
  • Ligand: CHOLESTEROL
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHITE ION
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human Na,K-ATPase alpha3/beta1/FXYD1

SupramoleculeName: Human Na,K-ATPase alpha3/beta1/FXYD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha-3

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Na+/K+-exchanging ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.864289 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE ILARDGPNAL TPPPTTPEWV KFCRQLFGG FSILLWIGAI LCFLAYGIQA GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA L VIREGEKM ...String:
MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE ILARDGPNAL TPPPTTPEWV KFCRQLFGG FSILLWIGAI LCFLAYGIQA GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA L VIREGEKM QVNAEEVVVG DLVEIKGGDR VPADLRIISA HGCKVDNSSL TGESEPQTRS PDCTHDNPLE TRNITFFSTN CV EGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIE IEHFIQLITG VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVA NVPEGL LATVTVCLTL TAKRMARKNC LVKNLEAVET LGSTSTICSD KTGTLTQNRM TVAHMWFDNQ IHEADTTEDQ SGTS FDKSS HTWVALSHIA GLCNRAVFKG GQDNIPVLKR DVAGDASESA LLKCIELSSG SVKLMRERNK KVAEIPFNST NKYQL SIHE TEDPNDNRYL LVMKGAPERI LDRCSTILLQ GKEQPLDEEM KEAFQNAYLE LGGLGERVLG FCHYYLPEEQ FPKGFA FDC DDVNFTTDNL CFVGLMSMID PPRAAVPDAV GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNI PV SQVNPRDAKA CVIHGTDLKD FTSEQIDEIL QNHTEIVFAR TSPQQKLIIV EGCQRQGAIV AVTGDGVNDS PALKKADI G VAMGIAGSDV SKQAADMILL DDNFASIVTG VEEGRLIFDN LKKSIAYTLT SNIPEITPFL LFIMANIPLP LGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLE DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF EETALAAFLS Y CPGMDVAL RMYPLKPSWW FCAFPYSFLI FVYDEIRKLI LRRNPGGWVE KETYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha-3

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Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-1

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.232566 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MARSHHHHHH HHHHPRRSRG KAKEEGSWKK FIWNSEKKEF LGRTGGSWFK ILLFYVIFYG CLAGIFIGTI QVMLLTISEF KPTYQDRVA PPGLTQIPQI QKTEISFRPN DPKSYEAYVL NIVRFLEKYK DSAQRDDMIF EDCGDVPSEP KERGDFNHER G ERKVCRFK ...String:
MARSHHHHHH HHHHPRRSRG KAKEEGSWKK FIWNSEKKEF LGRTGGSWFK ILLFYVIFYG CLAGIFIGTI QVMLLTISEF KPTYQDRVA PPGLTQIPQI QKTEISFRPN DPKSYEAYVL NIVRFLEKYK DSAQRDDMIF EDCGDVPSEP KERGDFNHER G ERKVCRFK LEWLGNCSGL NDETYGYKEG KPCIIIKLNR VLGFKPKPPK NESLETYPVM KYNPNVLPVQ CTGKRDEDKD KV GNVEYFG LGNSPGFPLQ YYPYYGKLLQ PKYLQPLLAV QFTNLTMDTE IRIECKAYGE NIGYSEKDRF QGRFDVKIEV KS

UniProtKB: Sodium/potassium-transporting ATPase subunit beta-1

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Macromolecule #3: Phospholemman

MacromoleculeName: Phospholemman / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.754979 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GTKAESPKEH DPFTYDYQSL QIGGLVIAGI LFILGILIVL SRRCRCKFNQ QQRTGEPDEE EGTFRSSIRR LSTRRR

UniProtKB: Phospholemman

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: PHOSPHITE ION

MacromoleculeName: PHOSPHITE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: PO3
Molecular weightTheoretical: 78.972 Da
Chemical component information

ChemComp-PO3:
PHOSPHITE ION

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Macromolecule #7: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 7 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4S3-(Morpholin-4-yl)propane-1-sulfonic acid
150.0 mMNaClsodium chloride
20.0 mMKClPotassium chloride
3.0 mMMgCl2magnesium chloride
1.0 mMC10H16N5O13P3Adenosine 5-triphosphate
0.015 mg/mlC47H88O22Lauryl maltose neopentyl glycol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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: 1.8 µm / Nominal defocus min: 0.6 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168521
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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