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.
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Change history
20 July 2011
A PDB accession code was corrected
References
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)
Hille, B. Ion Channels of Excitable Membranes 3rd edn (Sinauer Associates, 2001)
Ryan, D. P. & Ptacek, L. J. Episodic neurological channelopathies. Neuron 68, 282–292 (2010)
Catterall, W. A. Common modes of drug action on Na+ channels: local anesthetics, antiarrhythmics and anticonvulsants. Trends Pharmacol. Sci. 8, 57–65 (1987)
Yu, F. H. & Catterall, W. A. The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis. Sci. STKE 2004, re15 (2004)
Bezanilla, F. The action potential: from voltage-gated conductances to molecular structures. Biol. Res. 39, 425–435 (2006)
Catterall, W. A. Ion channel voltage sensors: structure, function, and pathophysiology. Neuron 67, 915–928 (2010)
Long, S. B., Campbell, E. B. & Mackinnon, R. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309, 897–903 (2005)
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)
Ren, D. et al. A prokaryotic voltage-gated sodium channel. Science 294, 2372–2375 (2001)
Koishi, R. et al. A superfamily of voltage-gated sodium channels in bacteria. J. Biol. Chem. 279, 9532–9538 (2004)
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)
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)
Curtis, B. M. & Catterall, W. A. Reconstitution of the voltage-sensitive calcium channel purified from skeletal muscle transverse tubules. Biochemistry 25, 3077–3083 (1986)
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)
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)
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)
Catterall, W. A. Molecular properties of voltage-sensitive sodium channels. Annu. Rev. Biochem. 55, 953–985 (1986)
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)
Tao, X., Lee, A., Limapichat, W., Dougherty, D. A. & MacKinnon, R. A gating charge transfer center in voltage sensors. Science 328, 67–73 (2010)
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)
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)
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)
Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998)
Jogini, V. & Roux, B. Electrostatics of the intracellular vestibule of K+ channels. J. Mol. Biol. 354, 272–288 (2005)
Hille, B. The permeability of the sodium channel to organic cations in myelinated nerve. J. Gen. Physiol. 58, 599–619 (1971)
Hille, B. The permeability of the sodium channel to metal cations in myelinated nerve. J. Gen. Physiol. 59, 637–658 (1972)
McCleskey, E. W. & Almers, W. The Ca channel in skeletal muscle is a large pore. Proc. Natl Acad. Sci. USA 82, 7149–7153 (1985)
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)
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)
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)
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)
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)
Hille, B. Ionic selectivity, saturation, and block in sodium channels. A four-barrier model. J. Gen. Physiol. 66, 535–560 (1975)
Morais-Cabral, J. H., Zhou, Y. & MacKinnon, R. Energetic optimization of ion conduction rate by the K+ selectivity filter. Nature 414, 37–42 (2001)
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)
Alam, A. & Jiang, Y. Structural analysis of ion selectivity in the NaK channel. Nature Struct. Mol. Biol. 16, 35–41 (2009)
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)
Harding, M. M. Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr. D 58, 872–874 (2002)
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)
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)
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)
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)
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)
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)
Hille, B. Local anesthetics: hydrophilic and hydrophobic pathways for the drug-receptor reaction. J. Gen. Physiol. 69, 497–515 (1977)
Oliver, D. et al. Functional conversion between A-type and delayed rectifier K+ channels by membrane lipids. Science 304, 265–270 (2004)
Delmas, P., Coste, B., Gamper, N. & Shapiro, M. S. Phosphoinositide lipid second messengers: new paradigms for calcium channel modulation. Neuron 47, 179–182 (2005)
Morello, R. S., Begenisich, T. & Yeh, J. Z. Determination of the active form of phenytoin. J. Pharmacol. Exp. Ther. 230, 156–161 (1984)
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)
Koth, C. M. & Payandeh, J. Strategies for the cloning and expression of membrane proteins. Adv. Protein Chem. Struct. Biol. 76, 43–86 (2009)
Cronin, C. N., Lim, K. B. & Rogers, J. Production of selenomethionyl-derivatized proteins in baculovirus-infected insect cells. Protein Sci. 16, 2023–2029 (2007)
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)
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)
Faham, S. et al. Crystallization of bacteriorhodopsin from bicelle formulations at room temperature. Protein Sci. 14, 836–840 (2005)
Otwinowski, Z. & Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode Vol. 276 (Academic, 1997)
CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)
Terwilliger, T. SOLVE and RESOLVE: automated structure solution and density modification. Meth. Enzymol. 374, 22–37 (2003)
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)
Brünger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)
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)
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)
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)
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)
Kleywegt, G. J. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D 52, 842–857 (1996)
DeLano, W. L. PyMOL molecular viewer (v. 1. 2r3pre) 〈http://www.pymol.org〉 (2002)
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.).
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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.
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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
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DOI: https://doi.org/10.1038/nature10238
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