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.

  • Article
  • Published:

The crystal structure of a voltage-gated sodium channel

This article has been updated

Abstract

Voltage-gated sodium (NaV) channels initiate electrical signalling in excitable cells and are the molecular targets for drugs and disease mutations, but the structural basis for their voltage-dependent activation, ion selectivity and drug block is unknown. Here we report the crystal structure of a voltage-gated Na+ channel from Arcobacter butzleri (NavAb) captured in a closed-pore conformation with four activated voltage sensors at 2.7 Å resolution. The arginine gating charges make multiple hydrophilic interactions within the voltage sensor, including unanticipated hydrogen bonds to the protein backbone. Comparisons to previous open-pore potassium channel structures indicate that the voltage-sensor domains and the S4–S5 linkers dilate the central pore by pivoting together around a hinge at the base of the pore module. The NavAb selectivity filter is short, 4.6 Å wide, and water filled, with four acidic side chains surrounding the narrowest part of the ion conduction pathway. This unique structure presents a high-field-strength anionic coordination site, which confers Na+ selectivity through partial dehydration via direct interaction with glutamate side chains. Fenestrations in the sides of the pore module are unexpectedly penetrated by fatty acyl chains that extend into the central cavity, and these portals are large enough for the entry of small, hydrophobic pore-blocking drugs. This structure provides the template for understanding electrical signalling in excitable cells and the actions of drugs used for pain, epilepsy and cardiac arrhythmia at the atomic level.

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: Structure of NavAb and the activated VSD.
Figure 2: NavAb pore module.
Figure 3: Structure of the NavAb selectivity filter.
Figure 4: Membrane access to the central cavity in NavAb.
Figure 5: Model for activation gate opening.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 3RVY, 3RVZ and 3RW0.

Change history

  • 20 July 2011

    A PDB accession code was corrected

References

  1. Hodgkin, A. L. & Huxley, A. F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. (Lond.) 117, 500–544 (1952)

    Article  CAS  Google Scholar 

  2. Hille, B. Ion Channels of Excitable Membranes 3rd edn (Sinauer Associates, 2001)

    Google Scholar 

  3. Ryan, D. P. & Ptacek, L. J. Episodic neurological channelopathies. Neuron 68, 282–292 (2010)

    Article  CAS  PubMed  Google Scholar 

  4. Catterall, W. A. Common modes of drug action on Na+ channels: local anesthetics, antiarrhythmics and anticonvulsants. Trends Pharmacol. Sci. 8, 57–65 (1987)

    Article  CAS  Google Scholar 

  5. Yu, F. H. & Catterall, W. A. The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis. Sci. STKE 2004, re15 (2004)

    PubMed  Google Scholar 

  6. Bezanilla, F. The action potential: from voltage-gated conductances to molecular structures. Biol. Res. 39, 425–435 (2006)

    Article  CAS  PubMed  Google Scholar 

  7. Catterall, W. A. Ion channel voltage sensors: structure, function, and pathophysiology. Neuron 67, 915–928 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Long, S. B., Campbell, E. B. & Mackinnon, R. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309, 897–903 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Long, S. B., Tao, X., Campbell, E. B. & MacKinnon, R. Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450, 376–382 (2007)

    Article  ADS  CAS  PubMed  Google Scholar 

  10. Ren, D. et al. A prokaryotic voltage-gated sodium channel. Science 294, 2372–2375 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Koishi, R. et al. A superfamily of voltage-gated sodium channels in bacteria. J. Biol. Chem. 279, 9532–9538 (2004)

    Article  CAS  PubMed  Google Scholar 

  12. Zhao, Y., Scheuer, T. & Catterall, W. A. Reversed voltage-dependent gating of a bacterial sodium channel with proline substitutions in the S6 transmembrane segment. Proc. Natl Acad. Sci. USA 101, 17873–17878 (2004)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  13. Yue, L., Navarro, B., Ren, D., Ramos, A. & Clapham, D. E. The cation selectivity filter of the bacterial sodium channel, NaChBac. J. Gen. Physiol. 120, 845–853 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Curtis, B. M. & Catterall, W. A. Reconstitution of the voltage-sensitive calcium channel purified from skeletal muscle transverse tubules. Biochemistry 25, 3077–3083 (1986)

    Article  CAS  PubMed  Google Scholar 

  15. Feller, D. J., Talvenheimo, J. A. & Catterall, W. A. The sodium channel from rat brain. Reconstitution of voltage-dependent scorpion toxin binding in vesicles of defined lipid composition. J. Biol. Chem. 260, 11542–11547 (1985)

    CAS  PubMed  Google Scholar 

  16. DeCaen, P. G., Yarov-Yarovoy, V., Zhao, Y., Scheuer, T. & Catterall, W. A. Disulfide locking a sodium channel voltage sensor reveals ion pair formation during activation. Proc. Natl Acad. Sci. USA 105, 15142–15147 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  17. DeCaen, P. G., Yarov-Yarovoy, V., Sharp, E. M., Scheuer, T. & Catterall, W. A. Sequential formation of ion pairs during activation of a sodium channel voltage sensor. Proc. Natl Acad. Sci. USA 106, 22498–22503 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  18. Catterall, W. A. Molecular properties of voltage-sensitive sodium channels. Annu. Rev. Biochem. 55, 953–985 (1986)

    Article  CAS  PubMed  Google Scholar 

  19. Yarov-Yarovoy, V., Baker, D. & Catterall, W. A. Voltage sensor conformations in the open and closed states in ROSETTA structural models of K+ channels. Proc. Natl Acad. Sci. USA 103, 7292–7297 (2006)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tao, X., Lee, A., Limapichat, W., Dougherty, D. A. & MacKinnon, R. A gating charge transfer center in voltage sensors. Science 328, 67–73 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zagotta, W. N., Hoshi, T. & Aldrich, R. W. Shaker potassium channel gating. III: Evaluation of kinetic models for activation. J. Gen. Physiol. 103, 321–362 (1994)

    Article  CAS  PubMed  Google Scholar 

  22. Kuzmenkin, A., Bezanilla, F. & Correa, A. M. Gating of the bacterial sodium channel, NaChBac: voltage-dependent charge movement and gating currents. J. Gen. Physiol. 124, 349–356 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Zhao, Y., Yarov-Yarovoy, V., Scheuer, T. & Catterall, W. A. A gating hinge in Na+ channels; a molecular switch for electrical signaling. Neuron 41, 859–865 (2004)

    Article  CAS  PubMed  Google Scholar 

  24. 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  PubMed  Google Scholar 

  25. Jogini, V. & Roux, B. Electrostatics of the intracellular vestibule of K+ channels. J. Mol. Biol. 354, 272–288 (2005)

    Article  CAS  PubMed  Google Scholar 

  26. Hille, B. The permeability of the sodium channel to organic cations in myelinated nerve. J. Gen. Physiol. 58, 599–619 (1971)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Hille, B. The permeability of the sodium channel to metal cations in myelinated nerve. J. Gen. Physiol. 59, 637–658 (1972)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  28. McCleskey, E. W. & Almers, W. The Ca channel in skeletal muscle is a large pore. Proc. Natl Acad. Sci. USA 82, 7149–7153 (1985)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Heinemann, S. H., Terlau, H., Stuhmer, W., Imoto, K. & Numa, S. Calcium channel characteristics conferred on the sodium channel by single mutations. Nature 356, 441–443 (1992)

    Article  ADS  CAS  PubMed  Google Scholar 

  30. Favre, I., Moczydlowski, E. & Schild, L. On the structural basis for ionic selectivity among Na+, K+, and Ca2+ in the voltage-gated sodium channel. Biophys. J. 71, 3110–3125 (1996)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  31. Yang, J., Ellinor, P. T., Sather, W. A., Zhang, J. F. & Tsien, R. W. Molecular determinants of Ca2+ selectivity and ion permeation in L-type Ca2+ channels. Nature 366, 158–161 (1993)

    Article  ADS  CAS  PubMed  Google Scholar 

  32. Ellinor, P. T., Yang, J., Sather, W. A., Zhang, J. F. & Tsien, R. W. Ca2+ channel selectivity at a single locus for high-affinity Ca2+ interactions. Neuron 15, 1121–1132 (1995)

    Article  CAS  PubMed  Google Scholar 

  33. Chen, X. H., Bezprozvanny, I. & Tsien, R. W. Molecular basis of proton block of L-type Ca2+ channels. J. Gen. Physiol. 108, 363–374 (1996)

    Article  CAS  PubMed  Google Scholar 

  34. Hille, B. Ionic selectivity, saturation, and block in sodium channels. A four-barrier model. J. Gen. Physiol. 66, 535–560 (1975)

    Article  CAS  PubMed  Google Scholar 

  35. 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  PubMed  Google Scholar 

  36. Ye, S., Li, Y. & Jiang, Y. Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore. Nature Struct. Mol. Biol. 17, 1019–1023 (2010)

    Article  CAS  Google Scholar 

  37. Alam, A. & Jiang, Y. Structural analysis of ion selectivity in the NaK channel. Nature Struct. Mol. Biol. 16, 35–41 (2009)

    Article  CAS  Google Scholar 

  38. Doi, M. et al. Caged and clustered structures of endothelin inhibitor BQ123, cyclo(-d-Trp-d-Asp-Pro-d-Val-Leu-).Na+, forming five and six coordination bonds between sodium ions and peptides. Acta Crystallogr. D 57, 628–634 (2001)

    Article  CAS  PubMed  Google Scholar 

  39. Harding, M. M. Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr. D 58, 872–874 (2002)

    Article  PubMed  Google Scholar 

  40. Phillips, K., Dauter, Z., Murchie, A. I., Lilley, D. M. & Luisi, B. The crystal structure of a parallel-stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273, 171–182 (1997)

    Article  CAS  PubMed  Google Scholar 

  41. Eisenman, G. & Horn, R. Ionic selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membr. Biol. 76, 197–225 (1983)

    Article  CAS  PubMed  Google Scholar 

  42. Noda, M., Suzuki, H., Numa, S. & Stuhmer, W. A single point mutation confers tetrodotoxin and saxitoxin insensitivity on the sodium channel II. FEBS Lett. 259, 213–216 (1989)

    Article  CAS  PubMed  Google Scholar 

  43. Hockerman, G. H., Peterson, B. Z., Johnson, B. D. & Catterall, W. A. Molecular determinants of drug binding and action on L-type calcium channels. Annu. Rev. Pharmacol. Toxicol. 37, 361–396 (1997)

    Article  CAS  PubMed  Google Scholar 

  44. Ragsdale, D. S., McPhee, J. C., Scheuer, T. & Catterall, W. A. Molecular determinants of state-dependent block of Na+ channels by local anesthetics. Science 265, 1724–1728 (1994)

    Article  ADS  CAS  PubMed  Google Scholar 

  45. Ragsdale, D. S., McPhee, J. C., Scheuer, T. & Catterall, W. A. Common molecular determinants of local anesthetic, antiarrhythmic, and anticonvulsant block of voltage-gated Na+ channels. Proc. Natl Acad. Sci. USA 93, 9270–9275 (1996)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hille, B. Local anesthetics: hydrophilic and hydrophobic pathways for the drug-receptor reaction. J. Gen. Physiol. 69, 497–515 (1977)

    Article  CAS  PubMed  Google Scholar 

  47. Oliver, D. et al. Functional conversion between A-type and delayed rectifier K+ channels by membrane lipids. Science 304, 265–270 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  48. Delmas, P., Coste, B., Gamper, N. & Shapiro, M. S. Phosphoinositide lipid second messengers: new paradigms for calcium channel modulation. Neuron 47, 179–182 (2005)

    Article  CAS  PubMed  Google Scholar 

  49. Morello, R. S., Begenisich, T. & Yeh, J. Z. Determination of the active form of phenytoin. J. Pharmacol. Exp. Ther. 230, 156–161 (1984)

    CAS  PubMed  Google Scholar 

  50. Lee, S. Y., Banerjee, A. & MacKinnon, R. Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K+ channels. PLoS Biol. 7, e47 (2009)

    PubMed  Google Scholar 

  51. Koth, C. M. & Payandeh, J. Strategies for the cloning and expression of membrane proteins. Adv. Protein Chem. Struct. Biol. 76, 43–86 (2009)

    Article  CAS  PubMed  Google Scholar 

  52. Cronin, C. N., Lim, K. B. & Rogers, J. Production of selenomethionyl-derivatized proteins in baculovirus-infected insect cells. Protein Sci. 16, 2023–2029 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Chaptal, V. et al. Fluorescence Detection of Heavy Atom Labeling (FD-HAL): a rapid method for identifying covalently modified cysteine residues by phasing atoms. J. Struct. Biol. 171, 82–87 (2010)

    Article  CAS  PubMed  Google Scholar 

  54. Faham, S. & Bowie, J. U. Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J. Mol. Biol. 316, 1–6 (2002)

    Article  CAS  PubMed  Google Scholar 

  55. Faham, S. et al. Crystallization of bacteriorhodopsin from bicelle formulations at room temperature. Protein Sci. 14, 836–840 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Otwinowski, Z. & Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode Vol. 276 (Academic, 1997)

    Book  Google Scholar 

  57. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  58. Terwilliger, T. SOLVE and RESOLVE: automated structure solution and density modification. Meth. Enzymol. 374, 22–37 (2003)

    Article  CAS  Google Scholar 

  59. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  Google Scholar 

  61. 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  PubMed  Google Scholar 

  62. 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)

    Article  CAS  PubMed  Google Scholar 

  63. Petřek, M., Kosinova, P., Koca, J. & Otyepka, M. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 15, 1357–1363 (2007)

    Article  PubMed  Google Scholar 

  64. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kleywegt, G. J. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D 52, 842–857 (1996)

    Article  CAS  PubMed  Google Scholar 

  66. DeLano, W. L. PyMOL molecular viewer (v. 1. 2r3pre) 〈http://www.pymol.org〉 (2002)

Download references

Acknowledgements

We thank B. Hille for comments on a draft of the manuscript and members of the N.Z. and W.A.C. groups for their support throughout this project. We are grateful to investigators who provided genomic DNA and the beamline staff at the Advanced Light Source (BL8.2.1 and BL8.2.2) for their assistance during data collection. J.P. acknowledges support from a Canadian Institutes of Health Research fellowship and the encouragement of E. Payandeh. This work was supported by grants from the National Institutes of Health (R01 NS15751 and U01 NS058039 to W.A.C.) and by the Howard Hughes Medical Institute (N.Z.).

Author information

Authors and Affiliations

Authors

Contributions

N.Z. and W.A.C. are co-senior authors. J.P., N.Z. and W.A.C. conceived and J.P. conducted the protein purification and crystallization experiments. J.P. and N.Z. determined and analysed the structures of NavAb. J.P. and T.S. performed functional studies of NavAb. J.P., N.Z. and W.A.C. wrote the manuscript.

Corresponding authors

Correspondence to Ning Zheng or William A. Catterall.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Table 1, Supplementary Discussion, Supplementary Figures 1-13 with legends and additional references. (PDF 8716 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Payandeh, J., Scheuer, T., Zheng, N. et al. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358 (2011). https://doi.org/10.1038/nature10238

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10238

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