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Crystal structure of the sodium–potassium pump

Nature volume 450, pages 1043–1049 (2007)Cite this article

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 3.5 Å 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 α-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 β- and γ-subunits specific to the Na+,K+-ATPase are associated with transmembrane helices αM7/αM10 and αM9, respectively. The γ-subunit corresponds to a fragment of the V-type ATPase c subunit. The carboxy terminus of the α-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.

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Figure 1: Functional characterization of Na + ,K + -ATPase used for crystallization.
Figure 2: Crystal packing and electron-density map.
Figure 3: Architecture of the Na + ,K + -ATPase αβγ complex and the K + /Rb + sites.
Figure 4: Interactions between α and β and between α and γ transmembrane helices.
Figure 5: Structural comparison of the Na + ,K + ATPase with the Ca 2+ -ATPase.
Figure 6: The C-terminal switch.

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Acknowledgements

We thank E. Pohl, C. Schulze-Briese, and T. Tomizaki for extensive assistance with synchrotron data collection and Anna Marie Nielsen, Jytte Jørgensen, Kirsten Lykke Pedersen, and Lene Jacobsen for technical assistance. We are thankful to Hanne Poulsen, Anja P. Einholm, and Laure Yatime for discussion, and to Dr. Otto Hansen, University of Aarhus, for the γ-subunit specific polyclonal antibody. This work was supported financially through the DANSYNC programme, the Centre for Structural Biology of the Danish Research Council for Natural Sciences, and a Hallas-Møller stipend from the Novo-Nordisk Foundation (to P.N.), as well as by research grants from the Lundbeck Foundation, the Novo Nordisk Foundation (Fabrikant Vilhelm Pedersen og Hustrus Legat), and the Danish Medical Research Council (to B.V.). B.P.P. is supported by a fellowship from the Aarhus Graduate School of Science.

Author Contributions J.P.M. performed crystallization experiments, data collection and processing, structure determination and refinement, and structural analysis. B.P.P. assisted in data collection, structure determination and analysis. T.L.S. identified initial crystallization conditions. M.S.T.J. produced mutant enzyme and characterized it functionally. J.P. performed occlusion experiments and prepared and characterized Na+,K+-ATPase samples as required for crystallization. P.N., B.V., and J.P.A. supervised the project and analysed the structure. The paper was written by J.P.M., P.N., B.V., and J.P.A., P.N. and B.V. have contributed equally and with equal resources to the project.

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Author notes

  1. Thomas L.-M. Sørensen

    Present address: Present address: Diamond Light Source Ltd, Diamond House, Chilton, Didcot, Oxfordshire, OX11 0DE, UK.,

  2. Bente Vilsen and Poul Nissen: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre for Membrane Pumps in Cells and Disease—PUMPKIN, Danish National Research Foundation, and,,

    J. Preben Morth, Bjørn P. Pedersen, Mads S. Toustrup-Jensen, Janne Petersen, Jens Peter Andersen, Bente Vilsen & Poul Nissen

  2. Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark,

    J. Preben Morth, Bjørn P. Pedersen, Thomas L.-M. Sørensen & Poul Nissen

  3. Institute of Physiology and Biophysics, University of Aarhus, Ole Worms Allé, Blg. 1160, DK-8000 Aarhus C, Denmark ,

    Mads S. Toustrup-Jensen, Janne Petersen, Jens Peter Andersen & Bente Vilsen

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Additional information

The Na+,K+-ATPase has the PDB code 3B8E.

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Supplementary Figures

This file contains Supplementary Figures S1-S6 with Legends. (PDF 5267 kb)

Supplementary Movie

This file contains Supplementary Movie 1 entitled ‘Rotating model of pig renal Na+,K+-ATPase’ The movie shows the α1 β1 γ complex of the Na+,K+-ATPase from pig kidney. The α-subunit is in blue, β in wheat, γ in red, and the C-terminal switch of α in light red. The two Rb+ ions in the membrane are indicated by magenta spheres, and the MgF42- and Mg2+ bound at the cytoplasmic P domain are indicated by orange and grey spheres, respectively. (SWF 9309 kb)

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Morth, J., Pedersen, B., Toustrup-Jensen, M. et al. Crystal structure of the sodium–potassium pump. Nature 450, 1043–1049 (2007). https://doi.org/10.1038/nature06419

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