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- EMDB-69776: Cryo-EM structure of human sodium pump W931R mutant in K+-occlude... -

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Basic information

Entry
Database: EMDB / ID: EMD-69776
TitleCryo-EM structure of human sodium pump W931R mutant in K+-occluded E2-Pi state
Map data
Sample
  • Complex: human sodium pump W931R mutant in K+-occluded E2-Pi state
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-3
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: water
KeywordsP-type ATPase / sodium pump / mutant / micelle / hypomagnesimia / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 ...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 / intracellular sodium ion homeostasis / cardiac muscle cell action potential involved in contraction / response to glycoside / osmosensory signaling pathway / relaxation of cardiac muscle / 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 / transporter activator activity / sperm flagellum / Ion homeostasis / proton transmembrane transport / potassium ion transmembrane transport / T-tubule / protein localization to plasma membrane / sodium ion transmembrane transport / sarcolemma / melanosome / extracellular vesicle / ATPase binding / protein-folding chaperone binding / Potential therapeutics for SARS / basolateral plasma membrane / transmembrane transporter binding / protein-macromolecule adaptor activity / apical plasma membrane / postsynaptic density / protein stabilization / membrane raft / axon / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / plasma membrane
Similarity search - Function
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 ...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-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsFujimura R / Gopalasingam CC / Abe K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: On the mechanism of hypomagnesimia with treatment-resistant seizures cansed by variants of the Na+,K+-ATPase alpha1 subunit (ATP1A1)
Authors: Artigas P / Abe K
History
DepositionMar 17, 2026-
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_69776.png

Downloads & links

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Map

FileDownload / File: emd_69776.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

Slices (1/3)

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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: 0.214
Minimum - Maximum-1.1241161 - 1.9221823
Average (Standard dev.)-0.0006298784 (±0.028048012)
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_69776_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69776_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69776_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : human sodium pump W931R mutant in K+-occluded E2-Pi state

EntireName: human sodium pump W931R mutant in K+-occluded E2-Pi state
Components
  • Complex: human sodium pump W931R mutant in K+-occluded E2-Pi state
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha-1
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-3
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: human sodium pump W931R mutant in K+-occluded E2-Pi state

SupramoleculeName: human sodium pump W931R mutant in K+-occluded E2-Pi state
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 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: 108.652812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SMDDHKLSLD ELHRKYGTDL SRGLTSARAA EILARDGPNA LTPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQND NLYLGVVLSA VVIITGCFSY YQEAKSSKIM ESFKNMVPQQ ALVIRNGEKM SINAEEVVVG DLVEVKGGDR I PADLRIIS ...String:
SMDDHKLSLD ELHRKYGTDL SRGLTSARAA EILARDGPNA LTPPPTTPEW IKFCRQLFGG FSMLLWIGAI LCFLAYSIQA ATEEEPQND NLYLGVVLSA VVIITGCFSY YQEAKSSKIM ESFKNMVPQQ ALVIRNGEKM SINAEEVVVG DLVEVKGGDR I PADLRIIS ANGCKVDNSS LTGESEPQTR SPDFTNENPL ETRNIAFFST NCVEGTARGI VVYTGDRTVM GRIATLASGL EG GQTPIAA EIEHFIHIIT GVAVFLGVSF FILSLILEYT WLEAVIFLIG IIVANVPEGL LATVTVCLTL TAKRMARKNC LVK NLEAVE TLGSTSTICS DKTGTLTQNR MTVAHMWFDN QIHEADTTEN QSGVSFDKTS ATWLALSRIA GLCNRAVFQA NQEN LPILK RAVAGDASES ALLKCIELCC GSVKEMRERY AKIVEIPFNS TNKYQLSIHK NPNTSEPQHL LVMKGAPERI LDRCS SILL HGKEQPLDEE LKDAFQNAYL ELGGLGERVL GFCHLFLPDE QFPEGFQFDT DDVNFPIDNL CFVGLISMID PPRAAV PDA VGKCRSAGIK VIMVTGDHPI TAKAIAKGVG IISEGNETVE DIAARLNIPV SQVNPRDAKA CVVHGSDLKD MTSEQLD DI LKYHTEIVFA RTSPQQKLII VEGCQRQGAI VAVTGDGVND SPALKKADIG VAMGIAGSDV SKQAADMILL DDNFASIV T GVEEGRLIFD NLKKSIAYTL TSNIPEITPF LIFIIANIPL PLGTVTILCI DLGTDMVPAI SLAYEQAESD IMKRQPRNP KTDKLVNERL ISMAYGQIGM IQALGGFFTY FVILAENGFL PIHLLGLRVD WDDRWINDVE DSYGQQWTYE QRKIVEFTCH TAFFVSIVV VQRADLVICK TRRNSVFQQG MKNKILIFGL FEETALAAFL SYCPGMGVAL RMYPLKPTWW FCAFPYSLLI F VYDEVRKL IIRRRPGGWV EKETYY

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

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Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-3

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.24 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLAEWKLFIY NPTTGEFLGR TAKSWGLILL FYLVFYGFLA ALFSFTMWVM LQTLNDEVPK YRDQIPSPGL MVFPKPVTAL EYTFSRSDP TSYAGYIEDL KKFLKPYTLE EQKNLTVCPD GALFEQKGPV YVACQFPISL LQACSGMNDP DFGYSQGNPC I LVKMNRII ...String:
SLAEWKLFIY NPTTGEFLGR TAKSWGLILL FYLVFYGFLA ALFSFTMWVM LQTLNDEVPK YRDQIPSPGL MVFPKPVTAL EYTFSRSDP TSYAGYIEDL KKFLKPYTLE EQKNLTVCPD GALFEQKGPV YVACQFPISL LQACSGMNDP DFGYSQGNPC I LVKMNRII GLKPEGVPRI DCVSKNEDIP NVAVYPHNGM IDLKYFPYYG KKLHVGYLQP LVAVQVSFAP NNTGKEVTVE CK IDGSANL KSQDDRDKFL GRVMFKITAR A

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

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Macromolecule #3: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #6: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 6 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 71 / 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

Concentration5 mg/mL
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 229314
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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