Crystal structure of the sodium–potassium pump at 2.4 Å resolution


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 medium1,2. 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 Ca2+-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 α- and β-subunits and a regulatory FXYD protein3,4, all of which are highly homologous to human ones. The ATPase was fixed in a state analogous to E2·2K+·Pi, in which the ATPase has a high affinity for K+ and still binds Pi, as in the first crystal structure of pig kidney enzyme at 3.5 Å resolution5. Clearly visualized now at 2.4 Å resolution are coordination of K+ and associated water molecules in the transmembrane binding sites and a phosphate analogue (MgF42-) in the phosphorylation site. The crystal structure shows that the β-subunit has a critical role in K+ binding (although its involvement has previously been suggested6,7,8) and explains, at least partially, why the homologous Ca2+-ATPase counter-transports H+ rather than K+, despite the coordinating residues being almost identical.

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Figure 1: Architecture of Na+, K+-ATPase with bound MgF42- and K+.
Figure 2: Superimposition of the crystal structure of Na + , K + -ATPase on that of Ca 2+ -ATPase.
Figure 3: Transmembrane K + -binding sites.
Figure 4: Interactions among the α- and β- subunits and the FXYD protein at the extracellular surface of the membrane.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the structure reported in this work have been deposited in the Protein Data Bank under accession number 2ZXE.


  1. 1

    Albers, R. W. Biochemical aspects of active transport. Annu. Rev. Biochem. 36, 727–756 (1967)

    CAS  Article  Google Scholar 

  2. 2

    Post, R. L., Hegyvary, C. & Kume, S. Activation by adenosine triphosphate in the phosphorylation kinetics of sodium and potassium ion transport adenosine triphosphatase. J. Biol. Chem. 247, 6530–6540 (1972)

    CAS  PubMed  Google Scholar 

  3. 3

    Mahmmoud, Y. A., Vorum, H. & Cornelius, F. Identification of a phospholemman-like protein from shark rectal glands. Evidence for indirect regulation of Na,K-ATPase by protein kinase c via a novel member of the FXYDY family. J. Biol. Chem. 275, 35969–35977 (2000)

    CAS  Article  Google Scholar 

  4. 4

    Garty, H. & Karlish, S. J. Role of FXYD proteins in ion transport. Annu. Rev. Physiol. 68, 431–459 (2006)

    CAS  Article  Google Scholar 

  5. 5

    Morth, J. P. et al. Crystal structure of the sodium–potassium pump. Nature 450, 1043–1049 (2007)

    ADS  CAS  Article  Google Scholar 

  6. 6

    Lutsenko, S. & Kaplan, J. H. An essential role for the extracellular domain of the Na,K-ATPase β-subunit in cation occlusion. Biochemistry 32, 6737–6743 (1993)

    CAS  Article  Google Scholar 

  7. 7

    Hasler, U., Crambert, G., Horisberger, J. D. & Geering, K. Structural and functional features of the transmembrane domain of the Na,K-ATPase β subunit revealed by tryptophan scanning. J. Biol. Chem. 276, 16356–16364 (2001)

    CAS  Article  Google Scholar 

  8. 8

    Geering, K. The functional role of β subunits in oligomeric P-type ATPases. J. Bioenerg. Biomembr. 33, 425–438 (2001)

    CAS  Article  Google Scholar 

  9. 9

    Schack, V. R. et al. Identification and function of a cytoplasmic K+ site of the Na+, K+ -ATPase. J. Biol. Chem. 283, 27982–27990 (2008)

    CAS  Article  Google Scholar 

  10. 10

    Toyoshima, C., Nomura, H. & Tsuda, T. Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Nature 432, 361–368 (2004)

    ADS  CAS  Article  Google Scholar 

  11. 11

    Toyoshima, C., Nakasako, M., Nomura, H. & Ogawa, H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 405, 647–655 (2000)

    ADS  CAS  Article  Google Scholar 

  12. 12

    Jacobsen, M. D., Pedersen, P. A. & Jorgensen, P. L. Importance of Na,K-ATPase residue alpha 1-Arg544 in the segment Arg544-Asp567 for high-affinity binding of ATP, ADP, or MgATP. Biochemistry 41, 1451–1456 (2002)

    CAS  Article  Google Scholar 

  13. 13

    Toyoshima, C. & Mizutani, T. Crystal structure of the calcium pump with a bound ATP analogue. Nature 430, 529–535 (2004)

    ADS  CAS  Article  Google Scholar 

  14. 14

    Sørensen, T. L., Møller, J. V. & Nissen, P. Phosphoryl transfer and calcium ion occlusion in the calcium pump. Science 304, 1672–1675 (2004)

    ADS  Article  Google Scholar 

  15. 15

    Clausen, J. D., McIntosh, D. B., Vilsen, B., Woolley, D. G. & Andersen, J. P. Importance of conserved N-domain residues Thr441, Glu442, Lys515, Arg560, and Leu562 of sarcoplasmic reticulum Ca2+-ATPase for MgATP binding and subsequent catalytic steps. Plasticity of the nucleotide-binding site. J. Biol. Chem. 278, 20245–20258 (2003)

    CAS  Article  Google Scholar 

  16. 16

    Murphy, A. J. & Hoover, J. C. Inhibition of the Na,K-ATPase by fluoride. Parallels with its inhibition of the sarcoplasmic reticulum CaATPase. J. Biol. Chem. 267, 16995–17000 (1992)

    CAS  PubMed  Google Scholar 

  17. 17

    Jensen, A. M., Sørensen, T. L., Olesen, C., Møller, J. V. & Nissen, P. Modulatory and catalytic modes of ATP binding by the calcium pump. EMBO J. 25, 2305–2314 (2006)

    Article  Google Scholar 

  18. 18

    Toyoshima, C. & Nomura, H. Structural changes in the calcium pump accompanying the dissociation of calcium. Nature 418, 605–611 (2002)

    ADS  CAS  Article  Google Scholar 

  19. 19

    Brown, I. D. & Wu, K. K. Empirical parameters for calculating cation-oxygen bond valences. Acta Crystallogr. B 32, 1957–1959 (1976)

    Article  Google Scholar 

  20. 20

    Jewell-Motz, E. A. & Lingrel, J. B. Site-directed mutagenesis of the Na,K-ATPase: consequences of substitutions of negatively-charged amino acids localized in the transmembrane domains. Biochemistry 32, 13523–13530 (1993)

    CAS  Article  Google Scholar 

  21. 21

    Nielsen, J. M., Pedersen, P. A., Karlish, S. J. & Jorgensen, P. L. Importance of intramembrane carboxylic acids for occlusion of K+ ions at equilibrium in renal Na,K-ATPase. Biochemistry 37, 1961–1968 (1998)

    CAS  Article  Google Scholar 

  22. 22

    Vilsen, B. & Andersen, J. P. Mutation to the glutamate in the fourth membrane segment of Na+,K+-ATPase and Ca2+-ATPase affects cation binding from both sides of the membrane and destabilizes the occluded enzyme forms. Biochemistry 37, 10961–10971 (1998)

    CAS  Article  Google Scholar 

  23. 23

    Ogawa, H. & Toyoshima, C. Homology modeling of the cation binding sites of Na+K+-ATPase. Proc. Natl Acad. Sci. USA 99, 15977–15982 (2002)

    ADS  CAS  Article  Google Scholar 

  24. 24

    Ueno, T. & Sekine, T. Study on calcium transport by sarcoplasmic reticulum vesicles using fluorescence probes. J. Biochem. 84, 787–794 (1978)

    CAS  Article  Google Scholar 

  25. 25

    Pietrobon, D. Familial hemiplegic migraine. Neurotherapeutics 4, 274–284 (2007)

    CAS  Article  Google Scholar 

  26. 26

    de Carvalho Aguiar, P. et al. Mutations in the Na+/K+ -ATPase α3 gene ATP1A3 are associated with rapid-onset dystonia parkinsonism. Neuron 43, 169–175 (2004)

    Article  Google Scholar 

  27. 27

    Cornelius, F., Turner, N. & Christensen, H. R. Modulation of Na,K-ATPase by phospholipids and cholesterol. II. Steady-state and presteady-state kinetics. Biochemistry 42, 8541–8549 (2003)

    CAS  Article  Google Scholar 

  28. 28

    Sotomayor, C. P., Aguilar, L. F., Cuevas, F. J., Helms, M. K. & Jameson, D. M. Modulation of pig kidney Na+/K+-ATPase activity by cholesterol: role of hydration. Biochemistry 39, 10928–10935 (2000)

    CAS  Article  Google Scholar 

  29. 29

    Colonna, T. E., Huynh, L. & Fambrough, D. M. Subunit interactions in the Na,K-ATPase explored with the yeast two-hybrid system. J. Biol. Chem. 272, 12366–12372 (1997)

    CAS  Article  Google Scholar 

  30. 30

    Toyoshima, C. et al. Modeling of the inhibitory interaction of phospholamban with the Ca2+ ATPase. Proc. Natl Acad. Sci. USA 100, 467–472 (2003)

    ADS  CAS  Article  Google Scholar 

  31. 31

    Jones, L. R. Rapid preparation of canine cardiac sarcolemmal vesicles by sucrose flotation. Methods Enzymol. 157, 85–91 (1988)

    CAS  Article  Google Scholar 

  32. 32

    Skou, J. C. & Esmann, M. Preparation of membrane Na+,K+-ATPase from rectal glands of Squalus acanthias . Methods Enzymol. 156, 43–46 (1988)

    CAS  Article  Google Scholar 

  33. 33

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  34. 34

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  35. 35

    Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  Google Scholar 

  36. 36

    Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. & Dodson, E. J. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D 55, 247–255 (1999)

    CAS  Article  Google Scholar 

  37. 37

    Laskowski, R. A., Moss, D. S. & Thornton, J. M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049–1067 (1993)

    CAS  Article  Google Scholar 

  38. 38

    McDonald, I. K. & Thornton, J. M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777–793 (1994)

    CAS  Article  Google Scholar 

  39. 39

    Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991)

    Article  Google Scholar 

  40. 40

    Merritt, E. A. & Bacon, D. J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997)

    CAS  Article  Google Scholar 

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We thank M. Kawamoto and N. Shimizu for their help in data collection at BL41XU, SPring-8, and T. Tsuda for many aspects of this work. We are grateful to D. B. McIntosh for his help in improving the manuscript and H. R.Z. Christensen for technical assistance. Thanks are also due to G. Cramb for sharing sequencing results of the β-subunit with us before publication. This work was supported by a Specially Promoted Project Grant from the Ministry of Education, Culture, Sports, Science and Technology of Japan, to C.T., and grants from the Danish Medical Research Council, to F.C.

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Correspondence to Chikashi Toyoshima.

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Shinoda, T., Ogawa, H., Cornelius, F. et al. Crystal structure of the sodium–potassium pump at 2.4 Å resolution. Nature 459, 446–450 (2009).

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