Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution

Abstract

Ion transport proteins must remove an ion's hydration shell to coordinate the ion selectively on the basis of its size and charge. To discover how the K+ channel solves this fundamental aspect of ion conduction, we solved the structure of the KcsA K+ channel in complex with a monoclonal Fab antibody fragment at 2.0 Å resolution. Here we show how the K+ channel displaces water molecules around an ion at its extracellular entryway, and how it holds a K+ ion in a square antiprism of water molecules in a cavity near its intracellular entryway. Carbonyl oxygen atoms within the selectivity filter form a very similar square antiprism around each K+ binding site, as if to mimic the waters of hydration. The selectivity filter changes its ion coordination structure in low K+ solutions. This structural change is crucial to the operation of the selectivity filter in the cellular context, where the K+ ion concentration near the selectivity filter varies in response to channel gating.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Fab attachment and crystal packing.
Figure 2: Stereo view of electron density in the region of the K+ channel selectivity filter.
Figure 3: Stereo view of a hydrated K+ ion in the central cavity.
Figure 4: Potassium ion dehydration at the extracellular pore entryway.
Figure 5: High- and low-K+ structures of the selectivity filter (stereo views).
Figure 6: Biological significance of the K+-dependent structural change in the selectivity filter.

Similar content being viewed by others

References

  1. Hille, B. Ionic Channels of Excitable Membranes (Sinauer, Sunderland, 1992).

    Google Scholar 

  2. Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998).

    Article  ADS  CAS  Google Scholar 

  3. Morais-Cabral, J. H., Zhou, Y. & MacKinnon, R. Energetic optimization of ion conduction rate by the K+ selectivity filter. Nature 414, 37–42 (2001).

    Article  ADS  CAS  Google Scholar 

  4. Armstrong, C. M. Interaction of tetraethylammonium ion derivatives with the potassium channels of giant axons. J. Gen. Physiol. 58, 413–437 (1971).

    Article  CAS  Google Scholar 

  5. Liu, Y., Holmgren, M., Jurman, M. E. & Yellen, G. Gated access to the pore of a voltage-dependent K+ channel. Neuron 19, 175–184 (1997).

    Article  Google Scholar 

  6. Perozo, E., Cortes, D. M. & Cuello, L. G. Structural rearrangements underlying K+-channel activation gating. Science 285, 73–78 (1999).

    Article  CAS  Google Scholar 

  7. Ostermeier, C., Iwata, S., Ludwig, B. & Michel, H. Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase. Nature Struct. Biol. 2, 842–846 (1995).

    Article  CAS  Google Scholar 

  8. Ostermeier, C., Harrenga, A., Ermler, U. & Michel, H. Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody Fv fragment. Proc. Natl Acad. Sci. USA 94, 10547–10553 (1997).

    Article  ADS  CAS  Google Scholar 

  9. Braden, B. et al. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J. Mol. Biol. 243, 767–781 (1994).

    Article  CAS  Google Scholar 

  10. Roux, B. & MacKinnon, R. The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. Science 285, 100–102 (1999).

    Article  CAS  Google Scholar 

  11. Otting, G., Liepinsh, E. & Wuthrich, K. Protein hydration in aqueous solution. Science 254, 974–980 (1991).

    Article  ADS  CAS  Google Scholar 

  12. Speakman, J. C. Acid salts of carboxylic acids, crystals with some “very short” hydrogen bonds. Struct. Bonding (Berlin) 12, 141–199 (1972).

    Article  CAS  Google Scholar 

  13. Dobler, v. M., Dunitz, J. D. & Kilbourn, B. T. Die struktur des KNCS-Komplexes von nonactin. Helv. Chim. Acta 52, 2573–2583 (1969).

    Article  CAS  Google Scholar 

  14. Neupert-Laves, K. & Dobler, M. The crystal structure of a K+ complex of valinomycin. Helv. Chim. Acta 58, 432–442 (1975).

    Article  CAS  Google Scholar 

  15. Dunitz, J. D. & Dobler, M. in Biological Aspects of Inorganic Chemistry (eds Addison, A. W., Cullen, W. R., Dolphin, D. & James, B. R.) 113–140 (Wiley, New York, 1977).

    Google Scholar 

  16. Jencks, W. P. Catalysis in Chemistry and Enzymology (Dover, New York, 1987).

    Google Scholar 

  17. Swenson, R. P. Jr & Armstrong, C. M. K+ channels close more slowly in the presence of external K+ and Rb+. Nature 291, 427–429 (1981).

    Article  ADS  CAS  Google Scholar 

  18. Miller, C., Latorre, R. & Reisin, I. Coupling of voltage-dependent gating and Ba2+ block in the high-conductance, Ca2+-activated K+ channel. J. Gen. Physiol. 90, 427–449 (1987).

    Article  CAS  Google Scholar 

  19. Demo, S. D. & Yellen, G. Ion effects on gating of the Ca2+-activated K+ channel correlate with occupancy of the pore. Biophys. J. 61, 639–648 (1992).

    Article  ADS  CAS  Google Scholar 

  20. Hoshi, T., Zagotta, W. N. & Aldrich, R. W. Shaker potassium channel gating. I: Transitions near the open state. J. Gen. Physiol. 103, 249–278 (1994).

    Article  CAS  Google Scholar 

  21. Zheng, J. & Sigworth, F. J. Intermediate conductances during deactivation of heteromultimeric Shaker potassium channels. J. Gen. Physiol. 112, 457–474 (1998).

    Article  CAS  Google Scholar 

  22. Lu, T. et al. Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter. Nature Neurosci. 4, 239–246 (2001).

    Article  CAS  Google Scholar 

  23. Harlow, E. & Lane, D. Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1989).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Collaborative Computational Project, No. 4. The CCP4 Suite: Programs for X-ray crystallography. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  26. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

  27. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  30. Bacon, D. & Anderson, W. F. A fast algorithm for rendering space filling molecule pictures. J. Mol. Graph 6, 219–220 (1988).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the staff at the National Synchrotron Light Source X-25 and Cornell High Energy Synchrotron Source A1 and F1 for assistance, Y. Jiang for help and advice at many stages of this project, F. Weis-Garcia and M. Nussenzweig for advice and teaching monoclonal methods, R. Dutzler for lipid topology files, and F. Valiyaveetil and J. Dunitz for discussions. This project was supported by a grant from the National Institutes of Health to R.M. R.M. is an investigator in the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhou, Y., Morais-Cabral, J., Kaufman, A. et al. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution. Nature 414, 43–48 (2001). https://doi.org/10.1038/35102009

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35102009

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing