3KDP

Crystal structure of the sodium-potassium pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the sodium-potassium pump.

Morth, J.P.Pedersen, B.P.Toustrup-Jensen, M.S.Sorensen, T.L.Petersen, J.Andersen, J.P.Vilsen, B.Nissen, P.

(2007) Nature 450: 1043-1049

  • DOI: 10.1038/nature06419
  • Primary Citation of Related Structures:  
    3KDP, 3B8E

  • PubMed Abstract: 
  • The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3 ...

    The Na+,K+-ATPase generates electrochemical gradients for sodium and potassium that are vital to animal cells, exchanging three sodium ions for two potassium ions across the plasma membrane during each cycle of ATP hydrolysis. Here we present the X-ray crystal structure at 3.5 A resolution of the pig renal Na+,K+-ATPase with two rubidium ions bound (as potassium congeners) in an occluded state in the transmembrane part of the alpha-subunit. Several of the residues forming the cavity for rubidium/potassium occlusion in the Na+,K+-ATPase are homologous to those binding calcium in the Ca2+-ATPase of sarco(endo)plasmic reticulum. The beta- and gamma-subunits specific to the Na+,K+-ATPase are associated with transmembrane helices alphaM7/alphaM10 and alphaM9, respectively. The gamma-subunit corresponds to a fragment of the V-type ATPase c subunit. The carboxy terminus of the alpha-subunit is contained within a pocket between transmembrane helices and seems to be a novel regulatory element controlling sodium affinity, possibly influenced by the membrane potential.


    Organizational Affiliation

    Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit alpha-1A, D [auth C]998Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1B, E [auth D]286Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane Entity: Yes 
UniProt
Find proteins for P05027 (Sus scrofa)
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Go to UniProtKB:  P05027
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aC [auth G], F [auth H]27Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane Entity: Yes 
UniProt
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.93α = 90
b = 261.5β = 90
c = 334.78γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description