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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: 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 / steroid hormone binding / membrane repolarization during cardiac muscle cell action potential / P-type sodium:potassium-exchanging transporter activity / sodium ion 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 / steroid hormone binding / membrane repolarization during cardiac muscle cell action potential / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / regulation of calcium ion transmembrane transport / 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 / potassium ion binding / ATPase activator activity / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / phosphatase activity / Ion transport by P-type ATPases / lateral plasma membrane / intercalated disc / transporter activator activity / sperm flagellum / ATP metabolic process / cardiac muscle contraction / Ion homeostasis / 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 / MHC class II protein complex binding / extracellular vesicle / ATPase binding / regulation of gene expression / protein-folding chaperone binding / Potential therapeutics for SARS / basolateral plasma membrane / response to hypoxia / transmembrane transporter binding / protein-macromolecule adaptor activity / cell adhesion / apical plasma membrane / postsynaptic density / protein stabilization / 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
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-
UpdateMay 27, 2026-
Current statusMay 27, 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

Projections

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Slices (2/3)

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
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Half map: #1

Fileemd_65820_half_map_1.map
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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: 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: 108.845961 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 S(BFD)KTGTLTQN RMTVAHMWFD NQIHEADTTE NQSGVSFDKT SATWLALSRI AGLCNRAVFQ ANQENLPIL KRAVAGDASE SALLKCIELC CGSVKEMRER YAKIVEIPFN STNKYQLSIH KNPNTSEPQH LLVMKGAPER I LDRCSSIL LHGKEQPLDE ELKDAFQNAY LELGGLGERV LGFCHLFLPD EQFPEGFQFD TDDVNFPIDN LCFVGLISMI DP PRAAVPD AVGKCRSAGI KVIMVTGDHP ITAKAIAKGV GIISEGNETV EDIAARLNIP VSQVNPRDAK ACVVHGSDLK DMT SEQLDD ILKYHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI GVAMGIAGSD VSKQAADMIL LDDN FASIV TGVEEGRLIF DNLKKSIAYT LTSNIPEITP FLIFIIANIP LPLGTVTILC IDLGTDMVPA ISLAYEQAES DIMKR QPRN PKTDKLVNER LISMAYGQIG MIQALGGFFT YFVILAENGF LPIHLLGLRV DWDDRWINDV EDSYGQQWTY EQRKIV EFT CHTAFFVSIV VVQWADLVIC KTRRNSVFQQ GMKNKILIFG LFEETALAAF LSYCPGMGVA LRMYPLKPTW WFCAFPY SL LIFVYDEVRK 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: water

MacromoleculeName: water / type: ligand / ID: 6 / 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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