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- EMDB-54125: Human alpha1 Na+,K+-ATPase in the Na+-bound E1 state -

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Basic information

Entry
Database: EMDB / ID: EMD-54125
TitleHuman alpha1 Na+,K+-ATPase in the Na+-bound E1 state
Map datamain map, 3SD
Sample
  • Complex: Na+,K+-ATPase alpha1/beta1/FXYD1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Phospholemman
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsactive ion transport / P-type ATPase / Na/K-ATPase / E1 / MEMBRANE PROTEIN / METAL TRANSPORT
Function / homology
Function and homology information


negative regulation of protein glutathionylation / protein transport into plasma membrane raft / 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 / photoreceptor inner segment membrane / steroid hormone binding / sodium ion binding / membrane repolarization during cardiac muscle cell action potential ...negative regulation of protein glutathionylation / protein transport into plasma membrane raft / 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 / photoreceptor inner segment membrane / steroid hormone binding / sodium ion 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 / cardiac muscle cell action potential involved in contraction / osmosensory signaling pathway / 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 / regulation of sodium ion transport / chloride channel activity / ATPase activator activity / potassium ion binding / organelle membrane / phosphatase activity / 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 / muscle contraction / proton transmembrane transport / potassium ion transmembrane transport / T-tubule / protein localization to plasma membrane / sodium ion transmembrane transport / sarcolemma / caveola / intracellular calcium ion homeostasis / melanosome / regulation of gene expression / MHC class II protein complex 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 / postsynaptic density / membrane raft / protein heterodimerization activity / innate immune response / axon / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / 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 alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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_54125.png

Downloads & links

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Map

FileDownload / File: emd_54125.map.gz / Format: CCP4 / Size: 64 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.)
0.83 Å/pix.
x 256 pix.
= 212.224 Å		0.83 Å/pix.
x 256 pix.
= 212.224 Å		0.83 Å/pix.
x 256 pix.
= 212.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0393
Minimum - Maximum-0.17684613 - 0.3464459
Average (Standard dev.)0.0010594345 (±0.013086485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharp map, 3SD

Fileemd_54125_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: half map A, 3SD

Fileemd_54125_half_map_1.map
Annotationhalf map A, 3SD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B, 3SD

Fileemd_54125_half_map_2.map
Annotationhalf map 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 : Na+,K+-ATPase alpha1/beta1/FXYD1

EntireName: Na+,K+-ATPase alpha1/beta1/FXYD1
Components
  • Complex: Na+,K+-ATPase alpha1/beta1/FXYD1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Phospholemman
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Na+,K+-ATPase alpha1/beta1/FXYD1

SupramoleculeName: Na+,K+-ATPase alpha1/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-1

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-1 / 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: 113.012828 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGKGVGRDKY EPAAVSEQGD KKGKKGKKDR DMDELKKEVS MDDHKLSLDE LHRKYGTDLS RGLTSARAAE ILARDGPNAL TPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQNDN LYLGVVLSAV VIITGCFSYY QEAKSSKIME S FKNMVPQQ ...String:
MGKGVGRDKY EPAAVSEQGD KKGKKGKKDR DMDELKKEVS MDDHKLSLDE LHRKYGTDLS RGLTSARAAE ILARDGPNAL TPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQNDN LYLGVVLSAV VIITGCFSYY QEAKSSKIME S FKNMVPQQ ALVIRNGEKM SINAEEVVVG DLVEVKGGDR IPADLRIISA NGCKVDNSSL TGESEPQTRS PDFTNENPLE TR NIAFFST NCVEGTARGI VVYTGDRTVM GRIATLASGL EGGQTPIAAE IEHFIHIITG VAVFLGVSFF ILSLILEYTW LEA VIFLIG IIVANVPEGL LATVTVCLTL TAKRMARKNC LVKNLEAVET LGSTSTICSD KTGTLTQNRM TVAHMWFDNQ IHEA DTTEN QSGVSFDKTS ATWLALSRIA GLCNRAVFQA NQENLPILKR AVAGDASESA LLKCIELCCG SVKEMRERYA KIVEI PFNS TNKYQLSIHK NPNTSEPQHL LVMKGAPERI LDRCSSILLH GKEQPLDEEL KDAFQNAYLE LGGLGERVLG FCHLFL PDE QFPEGFQFDT DDVNFPIDNL CFVGLISMID PPRAAVPDAV GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNET VE DIAARLNIPV SQVNPRDAKA CVVHGSDLKD MTSEQLDDIL KYHTEIVFAR TSPQQKLIIV EGCQRQGAIV AVTGDGVN D SPALKKADIG VAMGIAGSDV SKQAADMILL DDNFASIVTG VEEGRLIFDN LKKSIAYTLT SNIPEITPFL IFIIANIPL PLGTVTILCI DLGTDMVPAI SLAYEQAESD IMKRQPRNPK TDKLVNERLI SMAYGQIGMI QALGGFFTYF VILAENGFLP IHLLGLRVD WDDRWINDVE DSYGQQWTYE QRKIVEFTCH TAFFVSIVVV QWADLVICKT RRNSVFQQGM KNKILIFGLF E ETALAAFL SYCPGMGVAL RMYPLKPTWW FCAFPYSLLI FVYDEVRKLI IRRRPGGWVE KETYY

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

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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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
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 (6k x 4k) / Average electron dose: 58.88 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: PDB ENTRY
PDB model - PDB ID:

3wgu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 89662
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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