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Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel

Abstract

Voltage-gated sodium (Nav) channels are essential for the rapid depolarization of nerve and muscle1, and are important drug targets2. Determination of the structures of Nav channels will shed light on ion channel mechanisms and facilitate potential clinical applications. A family of bacterial Nav channels, exemplified by the Na+-selective channel of bacteria (NaChBac)3, provides a useful model system for structure–function analysis. Here we report the crystal structure of NavRh, a NaChBac orthologue from the marine alphaproteobacterium HIMB114 (Rickettsiales sp. HIMB114; denoted Rh), at 3.05 Å resolution. The channel comprises an asymmetric tetramer. The carbonyl oxygen atoms of Thr 178 and Leu 179 constitute an inner site within the selectivity filter where a hydrated Ca2+ resides in the crystal structure. The outer mouth of the Na+ selectivity filter, defined by Ser 181 and Glu 183, is closed, as is the activation gate at the intracellular side of the pore. The voltage sensors adopt a depolarized conformation in which all the gating charges are exposed to the extracellular environment. We propose that NavRh is in an ‘inactivated’ conformation. Comparison of NavRh with NavAb4 reveals considerable conformational rearrangements that may underlie the electromechanical coupling mechanism of voltage-gated channels.

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Figure 1: The structure of Na v Rh exhibits a closed conformation.
Figure 2: A Ca 2+ ion is bound in the asymmetric selectivity filter of Na v Rh.
Figure 3: The VSDs of Na v Rh exhibit a depolarized conformation.
Figure 4: Molecular basis of charge transfer of VSDs.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of NavRh are deposited in Protein Data Bank under accession number 4DXW.

References

  1. 1

    Hille, B. Ion Channels of Excitable Membranes (Sinauer Associates, 2001)

    Google Scholar 

  2. 2

    Mantegazza, M., Curia, G., Biagini, G., Ragsdale, D. S. & Avoli, M. Voltage-gated sodium channels as therapeutic targets in epilepsy and other neurological disorders. Lancet Neurol. 9, 413–424 (2010)

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  ADS  Article  Google Scholar 

  4. 4

    Payandeh, J., Scheuer, T., Zheng, N. & Catterall, W. A. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358 (2011)

    CAS  Article  Google Scholar 

  5. 5

    Catterall, W. A. The molecular basis of neuronal excitability. Science 223, 653–661 (1984)

    CAS  ADS  Article  Google Scholar 

  6. 6

    Jiang, Y. et al. X-ray structure of a voltage-dependent K+ channel. Nature 423, 33–41 (2003)

    CAS  ADS  Article  Google Scholar 

  7. 7

    Long, S. B., Campbell, E. B. & Mackinnon, R. Voltage sensor of Kv1.2: structural basis of electromechanical coupling. Science 309, 903–908 (2005)

    CAS  ADS  Article  Google Scholar 

  8. 8

    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)

    CAS  ADS  Article  Google Scholar 

  9. 9

    Butterwick, J. A. & MacKinnon, R. Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. J. Mol. Biol. 403, 591–606 (2010)

    CAS  Article  Google Scholar 

  10. 10

    Armstrong, C. M. & Bezanilla, F. Charge movement associated with the opening and closing of the activation gates of the Na channels. J. Gen. Physiol. 63, 533–552 (1974)

    CAS  Article  Google Scholar 

  11. 11

    Aggarwal, S. K. & MacKinnon, R. Contribution of the S4 segment to gating charge in the Shaker K+ channel. Neuron 16, 1169–1177 (1996)

    CAS  Article  Google Scholar 

  12. 12

    Seoh, S. A., Sigg, D., Papazian, D. M. & Bezanilla, F. Voltage-sensing residues in the S2 and S4 segments of the Shaker K+ channel. Neuron 16, 1159–1167 (1996)

    CAS  Article  Google Scholar 

  13. 13

    Vassilev, P. M., Scheuer, T. & Catterall, W. A. Identification of an intracellular peptide segment involved in sodium channel inactivation. Science 241, 1658–1661 (1988)

    CAS  ADS  Article  Google Scholar 

  14. 14

    Armstrong, C. M. & Bezanilla, F. Currents related to movement of the gating particles of the sodium channels. Nature 242, 459–461 (1973)

    CAS  ADS  Article  Google Scholar 

  15. 15

    Hoshi, T., Zagotta, W. N. & Aldrich, R. W. Biophysical and molecular mechanisms of Shaker potassium channel inactivation. Science 250, 533–538 (1990)

    CAS  ADS  Article  Google Scholar 

  16. 16

    Zagotta, W. N., Hoshi, T. & Aldrich, R. W. Restoration of inactivation in mutants of Shaker potassium channels by a peptide derived from ShB. Science 250, 568–571 (1990)

    CAS  ADS  Article  Google Scholar 

  17. 17

    Ulbricht, W. Sodium channel inactivation: molecular determinants and modulation. Physiol. Rev. 85, 1271–1301 (2005)

    CAS  Article  Google Scholar 

  18. 18

    Todt, H., Dudley, S. C., Jr, Kyle, J. W., French, R. J. & Fozzard, H. A. Ultra-slow inactivation in mu1 Na+ channels is produced by a structural rearrangement of the outer vestibule. Biophys. J. 76, 1335–1345 (1999)

    CAS  Article  Google Scholar 

  19. 19

    Yellen, G., Sodickson, D., Chen, T. Y. & Jurman, M. E. An engineered cysteine in the external mouth of a K+ channel allows inactivation to be modulated by metal binding. Biophys. J. 66, 1068–1075 (1994)

    CAS  Article  Google Scholar 

  20. 20

    Durell, S. R. & Guy, H. R. A putative prokaryote voltage-gated Ca2+ channel with only one 6TM motif per subunit. Biochem. Biophys. Res. Commun. 281, 741–746 (2001)

    CAS  Article  Google Scholar 

  21. 21

    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)

    CAS  Article  Google Scholar 

  22. 22

    Pavlov, E. et al. The pore, not cytoplasmic domains, underlies inactivation in a prokaryotic sodium channel. Biophys. J. 89, 232–242 (2005)

    CAS  ADS  Article  Google Scholar 

  23. 23

    Harding, M. M. The geometry of metal-ligand interactions relevant to proteins. Acta Crystallogr. D 55, 1432–1443 (1999)

    CAS  Article  Google Scholar 

  24. 24

    Shannon, R. D. Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta Crystallogr. A 32, 751–767 (1976)

    ADS  Article  Google Scholar 

  25. 25

    Hille, B. The hydration of sodium ions crossing the nerve membrane. Proc. Natl Acad. Sci. USA 68, 280–282 (1971)

    CAS  ADS  Article  Google Scholar 

  26. 26

    Armstrong, C. M. & Cota, G. Calcium ion as a cofactor in Na channel gating. Proc. Natl Acad. Sci. USA 88, 6528–6531 (1991)

    CAS  ADS  Article  Google Scholar 

  27. 27

    Schmidt, D., Cross, S. R. & MacKinnon, R. A gating model for the archeal voltage-dependent K+ channel KvAP in DPhPC and POPE:POPG decane lipid bilayers. J. Mol. Biol. 390, 902–912 (2009)

    CAS  Article  Google Scholar 

  28. 28

    Xiong, W., Li, R. A., Tian, Y. & Tomaselli, G. F. Molecular motions of the outer ring of charge of the sodium channel: do they couple to slow inactivation? J. Gen. Physiol. 122, 323–332 (2003)

    CAS  Article  Google Scholar 

  29. 29

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

    CAS  ADS  Article  Google Scholar 

  30. 30

    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)

    CAS  ADS  Article  Google Scholar 

  31. 31

    Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H. & Kraut, J. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 264, 1930–1935 (1994)

    CAS  ADS  Article  Google Scholar 

  32. 32

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

    CAS  Article  Google Scholar 

  33. 33

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

    Article  Google Scholar 

  34. 34

    Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  Google Scholar 

  35. 35

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

  36. 36

    Cowtan, K. dm: an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994)

    Google Scholar 

  37. 37

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  38. 38

    Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  Google Scholar 

  39. 39

    DeLano, W. L. The PyMOL Molecular Graphics System. Pymolhttp://www.pymol.org (2002)

  40. 40

    Smart, O. S., Goodfellow, J. M. & Wallace, B. A. The pore dimensions of gramicidin A. Biophys. J. 65, 2455–2460 (1993)

    CAS  Article  Google Scholar 

  41. 41

    Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195–201 (2006)

    CAS  Article  Google Scholar 

  42. 42

    Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381–3385 (2003)

    CAS  Article  Google Scholar 

  43. 43

    Guex, N. & Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997)

    CAS  Article  Google Scholar 

  44. 44

    Echols, N., Milburn, D. & Gerstein, M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31, 478–482 (2003)

    CAS  Article  Google Scholar 

  45. 45

    Krebs, W. G. & Gerstein, M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28, 1665–1675 (2000)

    CAS  Article  Google Scholar 

  46. 46

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

    CAS  Article  Google Scholar 

  47. 47

    Brunger, A. T. Version 1.2 of the Crystallography and NMR system. Nature Protocols 2, 2728–2733 (2007)

    CAS  Article  Google Scholar 

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Acknowledgements

We thank R. MacKinnon at Rockefeller University for discussions and reading the manuscript. We thank L. Feng at Rockefeller University for help. We thank S. Huang and F. Yu at Shanghai Synchrotron Radiation Facility beamline BL17U. K.H. acknowledges SPring-8 beamline BL41XU for proposal 2011A2039. This work was supported by funds from the Ministry of Science and Technology (grant numbers 2009CB918802, 2011CB910501 and 2011CB911102), projects 31125009 and 91017011 of the National Natural Science Foundation of China, and funds from Tsinghua University.

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X.Z., W.R., P.D., X.T., D.E.C. and N.Y. designed experiments. X.Z., W.R., P.D., C.Y., X.T., L.T., J.W., K.H., T.K., J.H., J.W. and N.Y. performed the experiments. X.Z., W.R., P.D., C.Y., X.T., J.W., D.E.C. and N.Y. analysed the data. X.Z., P.D., X.T., C.Y., J.W. and D.E.C. contributed to manuscript preparation. N.Y. wrote the manuscript.

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Correspondence to Nieng Yan.

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This file contains Supplementary Figures 1-10, Supplementary Tables 1-2 and the full legend for Supplementary Movie 1. (PDF 3407 kb)

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This file contains Supplementary Movie 1 which illustrates the structural basis for gating charge transfer. (MPG 16744 kb)

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Zhang, X., Ren, W., DeCaen, P. et al. Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel. Nature 486, 130–134 (2012). https://doi.org/10.1038/nature11054

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