4HQJ

Crystal structure of Na+,K+-ATPase in the Na+-bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state.

Nyblom, M.Poulsen, H.Gourdon, P.Reinhard, L.Andersson, M.Lindahl, E.Fedosova, N.Nissen, P.

(2013) Science 342: 123-127

  • DOI: https://doi.org/10.1126/science.1243352
  • Primary Citation of Related Structures:  
    4HQJ

  • PubMed Abstract: 

    The Na(+), K(+)-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na(+) and K(+) across the plasma membrane--a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K(+)-bound or ouabain-blocked forms. We present the crystal structure of a Na(+)-bound Na(+), K(+)-ATPase as determined at 4.3 Å resolution. Compared with the K(+)-bound form, large conformational changes are observed in the α subunit whereas the β and γ subunit structures are maintained. The locations of the three Na(+) sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na(+) from IIIb through IIIa, followed by exchange of Na(+) for K(+) at sites I and II, is suggested.


  • Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, DK-8000 Aarhus, Denmark.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A,
D [auth C]
1,021Sus scrofaMutation(s): 0 
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P05024 (Sus scrofa)
Explore P05024 
Go to UniProtKB:  P05024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05024
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1B,
E [auth D]
303Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Entity Groups  
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UniProt GroupP05027
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aC [auth G],
F [auth E]
65Sus scrofaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Entity Groups  
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UniProt GroupQ58K79
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CLR
Query on CLR

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M [auth A],
N [auth A],
U [auth C],
V [auth C],
W [auth D]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
ALF
Query on ALF

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H [auth A],
P [auth C]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG
Query on MG

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I [auth A],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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J [auth A]
K [auth A]
L [auth A]
R [auth C]
S [auth C]
J [auth A],
K [auth A],
L [auth A],
R [auth C],
S [auth C],
T [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.073α = 90
b = 219.578β = 90
c = 261.958γ = 90
Software Package:
Software NamePurpose
remdaq.pilatusdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2014-09-10
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary