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- EMDB-65820: Cryo-EM structure of a human sodium pump wildtype in ouabain-boun... -

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Basic information

Entry
Database: EMDB / ID: EMD-65820
TitleCryo-EM structure of a human sodium pump wildtype in ouabain-bound E2P state
Map data
Sample
  • Complex: human sodium pump alpha1/beta1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: OUABAIN
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: water
KeywordsP-type ATPase / Na+ / K+ / ATPase / Na/K-ATPase / cation pump / transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / sodium ion binding / membrane repolarization during cardiac muscle cell action potential / P-type sodium:potassium-exchanging transporter activity / steroid hormone binding / sodium:potassium-exchanging ATPase complex ...protein transport into plasma membrane raft / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / photoreceptor inner segment membrane / sodium ion binding / membrane repolarization during cardiac muscle cell action potential / P-type sodium:potassium-exchanging transporter activity / steroid hormone binding / 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 / cardiac muscle cell action potential involved in contraction / response to glycoside / osmosensory signaling pathway / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / Basigin interactions / cellular response to steroid hormone stimulus / organelle membrane / regulation of sodium ion transport / ATPase activator activity / potassium ion binding / phosphatase activity / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / Ion transport by P-type ATPases / intercalated disc / lateral plasma membrane / transporter activator activity / sperm flagellum / cardiac muscle contraction / ATP metabolic process / Ion homeostasis / proton transmembrane transport / T-tubule / protein localization to plasma membrane / potassium ion transmembrane transport / sodium ion transmembrane transport / sarcolemma / caveola / intracellular calcium ion homeostasis / regulation of gene expression / melanosome / MHC class II protein complex binding / ATPase binding / protein-folding chaperone binding / extracellular vesicle / response to hypoxia / Potential therapeutics for SARS / basolateral plasma membrane / transmembrane transporter binding / protein-macromolecule adaptor activity / postsynaptic density / protein stabilization / apical plasma membrane / membrane raft / protein heterodimerization activity / axon / lysosomal membrane / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / plasma membrane
Similarity search - Function
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 ...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
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: 2.39 Å
AuthorsAbe K / Gopalasingam CC
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Passive aberrant currents are induced by all Na pump variants causing hypomagnesemia
Authors: Artigas P / Abe K
History
DepositionAug 12, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65820.png

Downloads & links

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Map

FileDownload / File: emd_65820.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 450 pix.
= 338.4 Å		0.75 Å/pix.
x 450 pix.
= 338.4 Å		0.75 Å/pix.
x 450 pix.
= 338.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067
Minimum - Maximum-0.6664665 - 0.94067425
Average (Standard dev.)-0.00006458077 (±0.012640894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65820_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_65820_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_65820_half_map_2.map
Projections & Slices
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Sample components

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Entire : human sodium pump alpha1/beta1

EntireName: human sodium pump alpha1/beta1
Components
  • Complex: human sodium pump alpha1/beta1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
  • Ligand: SODIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: OUABAIN
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: water

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Supramolecule #1: human sodium pump alpha1/beta1

SupramoleculeName: human sodium pump alpha1/beta1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135 KDa

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

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.108258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG ...String:
MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISEFKPTYQD RVAPPGLTQI PQIQKTEIS FRPNDPKSYE AYVLNIVRFL EKYKDSAQRD DMIFEDCGDV PSEPKERGDF NHERGERKVC RFKLEWLGNC S GLNDETYG YKEGKPCIII KLNRVLGFKP KPPKNESLET YPVMKYNPNV LPVQCTGKRD EDKDKVGNVE YFGLGNSPGF PL QYYPYYG KLLQPKYLQP LLAVQFTNLT MDTEIRIECK AYGENIGYSE KDRFQGRFDV KIEVKS

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

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

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Na+/K+-exchanging ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 108.780961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VSMDDHKLSL DELHRKYGTD LSRGLTSARA AEILARDGPN ALTPPPTTPE WIKFCRQLFG GFSMLLWIGA ILCFLAYSIQ AATEEEPQN DNLYLGVVLS AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIRNGEK MSINAEEVVV GDLVEVKGGD R IPADLRII ...String:
VSMDDHKLSL DELHRKYGTD LSRGLTSARA AEILARDGPN ALTPPPTTPE WIKFCRQLFG GFSMLLWIGA ILCFLAYSIQ AATEEEPQN DNLYLGVVLS AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIRNGEK MSINAEEVVV GDLVEVKGGD R IPADLRII SANGCKVDNS SLTGESEPQT RSPDFTNENP LETRNIAFFS TNCVEGTARG IVVYTGDRTV MGRIATLASG LE GGQTPIA AEIEHFIHII TGVAVFLGVS FFILSLILEY TWLEAVIFLI GIIVANVPEG LLATVTVCLT LTAKRMARKN CLV KNLEAV ETLGSTSTIC SDKTGTLTQN RMTVAHMWFD NQIHEADTTE NQSGVSFDKT SATWLALSRI AGLCNRAVFQ ANQE NLPIL KRAVAGDASE SALLKCIELC CGSVKEMRER YAKIVEIPFN STNKYQLSIH KNPNTSEPQH LLVMKGAPER ILDRC SSIL LHGKEQPLDE ELKDAFQNAY LELGGLGERV LGFCHLFLPD EQFPEGFQFD TDDVNFPIDN LCFVGLISMI DPPRAA VPD AVGKCRSAGI KVIMVTGDHP ITAKAIAKGV GIISEGNETV EDIAARLNIP VSQVNPRDAK ACVVHGSDLK DMTSEQL DD ILKYHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI GVAMGIAGSD VSKQAADMIL LDDNFASI V TGVEEGRLIF DNLKKSIAYT LTSNIPEITP FLIFIIANIP LPLGTVTILC IDLGTDMVPA ISLAYEQAES DIMKRQPRN PKTDKLVNER LISMAYGQIG MIQALGGFFT YFVILAENGF LPIHLLGLRV DWDDRWINDV EDSYGQQWTY EQRKIVEFTC HTAFFVSIV VVQWADLVIC KTRRNSVFQQ GMKNKILIFG LFEETALAAF LSYCPGMGVA LRMYPLKPTW WFCAFPYSLL I FVYDEVRK LIIRRRPGGW VEKETYY

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

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: OUABAIN

MacromoleculeName: OUABAIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: OBN
Molecular weightTheoretical: 584.652 Da
Chemical component information

ChemComp-OBN:
OUABAIN

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Macromolecule #6: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 25 / 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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (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: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4xe5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 473771
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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