9ROA | pdb_00009roa

Human alpha3 Na+,K+-ATPase in the Na+-occluded E1P-ADP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ROA

This is version 1.1 of the entry. See complete history

Literature

Active conformations of neuronal Na + , K + -ATPase isoforms and a disease-causing mutant.

Christensen, M.E.Habeck, M.Katz, A.Fruergaard, M.U.Peleg, Y.Pick, U.Karlish, S.J.D.Nissen, P.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75997-4
  • Primary Citation Related Structures: 
    9RO9, 9ROA, 9ROD, 9ROE, 9ROF, 9ROG, 9ROH, 9ROI, 9ROJ, 9ROK, 9ROL, 9ROM, 9RON, 9ROO, 9ROP, 9ROQ

  • PubMed 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 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 3 ]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.


  • Organizational Affiliation
    • Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 161.01 kDa 
  • Atom Count: 10,208 
  • Modeled Residue Count: 1,277 
  • Deposited Residue Count: 1,408 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-31,013Homo sapiensMutation(s): 0 
Gene Names: ATP1A3
EC: 7.2.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for P13637 (Homo sapiens)
Explore P13637 
Go to UniProtKB:  P13637
PHAROS:  P13637
GTEx:  ENSG00000105409 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13637
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1319Homo sapiensMutation(s): 0 
Gene Names: ATP1B1ATP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P05026 (Homo sapiens)
Explore P05026 
Go to UniProtKB:  P05026
PHAROS:  P05026
GTEx:  ENSG00000143153 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05026
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P05026-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholemman76Homo sapiensMutation(s): 0 
Gene Names: FXYD1PLM
UniProt & NIH Common Fund Data Resources
Find proteins for O00168 (Homo sapiens)
Explore O00168 
Go to UniProtKB:  O00168
PHAROS:  O00168
GTEx:  ENSG00000266964 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00168
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
F [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
N [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
A
L-PEPTIDE LINKINGC4 H8 N O7 PASP

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union793086
LundbeckfondenDenmarkR310-2018-3713
Novo Nordisk FoundationDenmarkNNF20OC0060483
The Carlsberg FoundationDenmarkCF22-1535
The Carlsberg FoundationDenmarkCF23-1394

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references