2ZXE

Crystal structure of the sodium - potassium pump in the E2.2K+.Pi state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the sodium - potassium pump at 2.4 A resolution

Shinoda, T.Ogawa, H.Cornelius, F.Toyoshima, C.

(2009) Nature 459: 446-450

  • DOI: 10.1038/nature07939

  • PubMed Abstract: 
  • Sodium-potassium ATPase is an ATP-powered ion pump that establishes concentration gradients for Na(+) and K(+) ions across the plasma membrane in all animal cells by pumping Na(+) from the cytoplasm and K(+) from the extracellular medium. Such gradie ...

    Sodium-potassium ATPase is an ATP-powered ion pump that establishes concentration gradients for Na(+) and K(+) ions across the plasma membrane in all animal cells by pumping Na(+) from the cytoplasm and K(+) from the extracellular medium. Such gradients are used in many essential processes, notably for generating action potentials. Na(+), K(+)-ATPase is a member of the P-type ATPases, which include sarcoplasmic reticulum Ca(2+)-ATPase and gastric H(+), K(+)-ATPase, among others, and is the target of cardiac glycosides. Here we describe a crystal structure of this important ion pump, from shark rectal glands, consisting of alpha- and beta-subunits and a regulatory FXYD protein, all of which are highly homologous to human ones. The ATPase was fixed in a state analogous to E2.2K(+).P(i), in which the ATPase has a high affinity for K(+) and still binds P(i), as in the first crystal structure of pig kidney enzyme at 3.5 A resolution. Clearly visualized now at 2.4 A resolution are coordination of K(+) and associated water molecules in the transmembrane binding sites and a phosphate analogue (MgF(4)(2-)) in the phosphorylation site. The crystal structure shows that the beta-subunit has a critical role in K(+) binding (although its involvement has previously been suggested) and explains, at least partially, why the homologous Ca(2+)-ATPase counter-transports H(+) rather than K(+), despite the coordinating residues being almost identical.


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na, K-ATPase alpha subunit
A
1028Squalus acanthiasMutation(s): 0 
Gene Names: atn1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for Q4H132 (Squalus acanthias)
Go to UniProtKB:  Q4H132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Na+,K+-ATPase beta subunit
B
305Squalus acanthiasMutation(s): 0 
Gene Names: atp1b1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for C4IX13 (Squalus acanthias)
Go to UniProtKB:  C4IX13
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Phospholemman-like protein
G
74Squalus acanthiasMutation(s): 0 
Gene Names: fxyd10
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Na,K-ATPase; shark
Find proteins for Q70Q12 (Squalus acanthias)
Go to UniProtKB:  Q70Q12
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MF4
Query on MF4

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Download CCD File 
A
TETRAFLUOROMAGNESATE(2-)
MAGNESIUMTETRAFLUORIDE
F4 Mg
XVYWAXYEHHUKQW-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

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B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 223.815α = 90.00
b = 50.914β = 105.12
c = 163.786γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance