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- PDB-9rog: Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obta... -

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Basic information

Entry
Database: PDB / ID: 9rog
TitleHuman alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state obtained under turnover conditions
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Phospholemman
KeywordsMETAL TRANSPORT / active ion transport / P-type ATPase / Na/K-ATPase / E1P / MEMBRANE PROTEIN
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 / membrane repolarization during cardiac muscle cell action potential ...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 / 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 / response to glycoside / regulation of heart contraction / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / Basigin interactions / cellular response to steroid hormone stimulus / chloride transport / organelle membrane / chloride channel activity / ATPase activator activity / neuronal cell body membrane / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / Ion transport by P-type ATPases / sodium channel regulator activity / lateral plasma membrane / intercalated disc / transporter activator activity / sperm flagellum / cardiac muscle contraction / ATP metabolic process / Ion homeostasis / neuron projection maintenance / proton transmembrane transport / photoreceptor inner segment / muscle contraction / 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 / ATPase binding / extracellular vesicle / protein-folding chaperone binding / response to hypoxia / Potential therapeutics for SARS / basolateral plasma membrane / cell adhesion / transmembrane transporter binding / protein-macromolecule adaptor activity / innate immune response / protein stabilization / apical plasma membrane / protein heterodimerization activity / axon / neuronal cell body / protein kinase binding / synapse / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / 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
ADENOSINE-5'-DIPHOSPHATE / CHOLESTEROL / PHOSPHITE ION / Phospholemman / Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-transporting ATPase subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChristensen, M.E. / Habeck, M. / Katz, A. / Fruergaard, M.U. / Karlish, S.J.D. / Nissen, P.
Funding supportEuropean Union, Denmark, 5items
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: Mads Eskesen Christensen / Michael Habeck / Adriana Katz / Marlene Uglebjerg Fruergaard / Yoav Peleg / Uri Pick / Steven J D Karlish / Poul Nissen /
Abstract: Na,K-ATPases establish and maintain the vital electrochemical gradients for Na and K across animal cell membranes. The protein is a ternary complex composed of α, β and FXYD subunits, of which ...Na,K-ATPases establish and maintain the vital electrochemical gradients for Na and K across animal cell membranes. The protein is a ternary complex composed of α, β and FXYD subunits, of which isoforms that fine-tune transport properties are expressed in a tissue-specific fashion. Here we report cryo-EM structures under active ATPase turn-over conditions of the ubiquitously expressed human α1β1FXYD1 and neuron-specific α3β1FXYD1 isoform complexes and probe their specific functional and biophysical properties. The data provides an extensive insight into Na-transport of ATP-activated enzyme through four distinct conformational states, including a sodium-bound phosphoenzyme intermediate, denoted [Na]E2P. This conformation reveals a crucial structural change that precedes Na release in the inward to outward (E1P-E2P) transition, within the general context of the sequential, active transport mechanism. We discuss the mechanism of the physiologically important differentiation in Na affinity of α3 compared to α1, the co-operative Na binding at the ion-binding sites, and the mechanistic aspects of cytoplasmic ion gating and extracellular Na release. Finally we present the structures of a disease-causing mutant form of α3, associated with Alternating Hemiplegia of Childhood (Q140L). The mutation compromises a specific phospholipid-binding pocket and impedes polyunsaturated phospholipid-mediated stimulation of Na,K-ATPase activity.
History
DepositionJun 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Sep 9, 2026Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/potassium-transporting ATPase subunit alpha-3
B: Sodium/potassium-transporting ATPase subunit beta-1
C: Phospholemman
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,22913
Polymers157,8523
Non-polymers2,37710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 2 molecules AB

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-3 / Na(+)/K(+) ATPase alpha-3 subunit / Na(+)/K(+) ATPase alpha(III) subunit / Sodium pump subunit alpha-3


Mass: 111864.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1A3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P13637, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 37232.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP1B1, ATP1B / Production host: Komagataella pastoris (fungus) / References: UniProt: P05026

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Protein / Sugars , 2 types, 4 molecules C

#3: Protein Phospholemman / FXYD domain-containing ion transport regulator 1 / Sodium/potassium-transporting ATPase subunit FXYD1


Mass: 8754.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXYD1, PLM / Production host: Escherichia coli (E. coli) / References: UniProt: O00168
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 7 molecules

#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Na,K-ATPase alpha3/beta1/FXYD1 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
41NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM3-(Morpholin-4-yl)propane-1-sulfonic acidC7H15NO4S1
2150 mMsodium chlorideNaCl1
320 mMPotassium chlorideKCl1
43 mMmagnesium chlorideMgCl21
51 mMAdenosine 5-triphosphateC10H16N5O13P31
60.015 mg/mlLauryl maltose neopentyl glycolC47H88O221
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168521 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310368
ELECTRON MICROSCOPYf_angle_d0.5514071
ELECTRON MICROSCOPYf_dihedral_angle_d7.1731429
ELECTRON MICROSCOPYf_chiral_restr0.0421607
ELECTRON MICROSCOPYf_plane_restr0.0031788

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