3B8E

Crystal structure of the sodium-potassium pump


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.277 

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This is version 1.1 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-r ...

    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-1AC998Sus scrofaMutation(s): 0 
Gene Names: ATP1A1
EC: 3.6.3.9 (PDB Primary Data), 7.2.2.13 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05024 (Sus scrofa)
Explore P05024 
Go to UniProtKB:  P05024
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/potassium-transporting ATPase subunit beta-1BD46Sus scrofaMutation(s): 0 
Gene Names: ATP1B1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for P05027 (Sus scrofa)
Explore P05027 
Go to UniProtKB:  P05027
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Na+/K+ ATPase gamma subunit transcript variant aGH29Sus scrofaMutation(s): 0 
Gene Names: FXYD2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; pig kidney
Find proteins for Q58K79 (Sus scrofa)
Explore Q58K79 
Go to UniProtKB:  Q58K79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download CCD File 
B, C
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
MF4
Query on MF4

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A, C
TETRAFLUOROMAGNESATE(2-)
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
RB
Query on RB

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A, C
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.277 
  • 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
SHARPphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance