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Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel

Abstract

Na+-activated K+ channels are members of the Slo family of large conductance K+ channels that are widely expressed in the brain, where their opening regulates neuronal excitability. These channels fulfil a number of biological roles and have intriguing biophysical properties, including conductance levels that are ten times those of most other K+ channels and gating sensitivity to intracellular Na+. Here we present the structure of a complete Na+-activated K+ channel, chicken Slo2.2, in the Na+-free state, determined by cryo-electron microscopy at a nominal resolution of 4.5 ångströms. The channel is composed of a large cytoplasmic gating ring, in which resides the Na+-binding site and a transmembrane domain that closely resembles voltage-gated K+ channels. In the structure, the cytoplasmic domain adopts a closed conformation and the ion conduction pore is also closed. The structure reveals features that can explain the unusually high conductance of Slo channels and how contraction of the cytoplasmic gating ring closes the pore.

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Figure 1: Cryo-EM structure of chicken Slo2.2.
Figure 2: Architecture of Slo2.2.
Figure 3: Interactions between pore and S1–S4 domains.
Figure 4: Slo2.2 ion conduction pathway.
Figure 5: Slo2.2 gating ring.
Figure 6: Slo2.2 gating.

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Electron Microscopy Data Bank

Protein Data Bank

Data deposits

The 3D cryo-EM density maps of Slo2.2 with low-pass filter and amplitude modification have been deposited in the Electron Microscopy Data Bank under accession numbers EMD-3062 (Slo2.2 whole channel), EMD-3063 (Slo2.2 gating ring) and EMD-3064 (Slo2.2 TMD). Atomic coordinates for the atomic model of full-length Slo2.2, Slo2.2 gating ring and Slo2.2 TMD have been deposited in the Protein Data Bank under accession numbers 5A6E, 5A6F and 5A6G, respectively.

References

  1. Hille, B. Ionic Channels of Excitable Membranes 3rd edn 131–168 (Sinauer Associates, 2001)

    Google Scholar 

  2. Bader, C. R., Bernheim, L. & Bertrand, D. Sodium-activated potassium current in cultured avian neurones. Nature 317, 540–542 (1985)

    Article  ADS  CAS  Google Scholar 

  3. Dryer, S. E., Fujii, J. T. & Martin, A. R. A Na+-activated K+ current in cultured brain stem neurones from chicks. J. Physiol. (Lond.) 410, 283–296 (1989)

    Article  CAS  Google Scholar 

  4. Haimann, C. & Bader, C. R. Sodium-activated potassium channel in avian sensory neurons. Cell Biol. Int. Rep. 13, 1133–1139 (1989)

    Article  CAS  Google Scholar 

  5. Kameyama, M. et al. Intracellular Na+ activates a K+ channel in mammalian cardiac cells. Nature 309, 354–356 (1984)

    Article  ADS  CAS  Google Scholar 

  6. Schwindt, P. C., Spain, W. J. & Crill, W. E. Long-lasting reduction of excitability by a sodium-dependent potassium current in cat neocortical neurons. J. Neurophysiol. 61, 233–244 (1989)

    Article  CAS  Google Scholar 

  7. Yan, Y., Yang, Y., Bian, S. & Sigworth, F. J. Expression, purification and functional reconstitution of slack sodium-activated potassium channels. J. Membr. Biol. 245, 667–674 (2012)

    Article  CAS  Google Scholar 

  8. Yuan, A. et al. The sodium-activated potassium channel is encoded by a member of the Slo gene family. Neuron 37, 765–773 (2003)

    Article  CAS  Google Scholar 

  9. Bhattacharjee, A., Gan, L. & Kaczmarek, L. K. Localization of the Slack potassium channel in the rat central nervous system. J. Comp. Neurol. 454, 241–254 (2002)

    Article  CAS  Google Scholar 

  10. Kaczmarek, L. K. et al. Regulation of the timing of MNTB neurons by short-term and long-term modulation of potassium channels. Hear. Res. 206, 133–145 (2005)

    Article  CAS  Google Scholar 

  11. Wallén, P. et al. Sodium-dependent potassium channels of a Slack-like subtype contribute to the slow afterhyperpolarization in lamprey spinal neurons. J. Physiol. (Lond.) 585, 75–90 (2007)

    Article  Google Scholar 

  12. Yang, B., Desai, R. & Kaczmarek, L. K. Slack and Slick KNa channels regulate the accuracy of timing of auditory neurons. J. Neurosci. 27, 2617–2627 (2007)

    Article  CAS  Google Scholar 

  13. Allen, A. S. et al. De novo mutations in epileptic encephalopathies. Nature 501, 217–221 (2013)

    Article  ADS  CAS  Google Scholar 

  14. Barcia, G. et al. De novo gain-of-function KCNT1 channel mutations cause malignant migrating partial seizures of infancy. Nature Genet. 44, 1255–1259 (2012)

    Article  CAS  Google Scholar 

  15. Ishii, A. et al. A recurrent KCNT1 mutation in two sporadic cases with malignant migrating partial seizures in infancy. Gene 531, 467–471 (2013)

    Article  CAS  Google Scholar 

  16. McTague, A. et al. Migrating partial seizures of infancy: expansion of the electroclinical, radiological and pathological disease spectrum. Brain 136, 1578–1591 (2013)

    Article  Google Scholar 

  17. Vanderver, A. et al. Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy. Pediatr. Neurol. 50, 112–114 (2014)

    Article  Google Scholar 

  18. Heron, S. E. et al. Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy. Nature Genet. 44, 1188–1190 (2012)

    Article  CAS  Google Scholar 

  19. Martin, H. C. et al. Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis. Hum. Mol. Genet. 23, 3200–3211 (2014)

    Article  CAS  Google Scholar 

  20. Huang, F. et al. TMEM16C facilitates Na+-activated K+ currents in rat sensory neurons and regulates pain processing. Nature Neurosci. 16, 1284–1290 (2013)

    Article  CAS  Google Scholar 

  21. Lu, R. et al. Slack channels expressed in sensory neurons control neuropathic pain in mice. J. Neurosci. 35, 1125–1135 (2015)

    Article  Google Scholar 

  22. Lu, S., Das, P., Fadool, D. A. & Kaczmarek, L. K. The Slack sodium-activated potassium channel provides a major outward current in olfactory neurons of Kv1.3−/− super-smeller mice. J. Neurophysiol. 103, 3311–3319 (2010)

    Article  CAS  Google Scholar 

  23. Paulais, M., Lachheb, S. & Teulon, J. A Na+- and Cl-activated K+ channel in the thick ascending limb of mouse kidney. J. Gen. Physiol. 127, 205–215 (2006)

    Article  CAS  Google Scholar 

  24. Wu, Y., Yang, Y., Ye, S. & Jiang, Y. Structure of the gating ring from the human large-conductance Ca2+-gated K+ channel. Nature 466, 393–397 (2010)

    Article  ADS  CAS  Google Scholar 

  25. Yuan, P., Leonetti, M. D., Hsiung, Y. & MacKinnon, R. Open structure of the Ca2+ gating ring in the high-conductance Ca2+-activated K+ channel. Nature 481, 94–97 (2012)

    Article  ADS  CAS  Google Scholar 

  26. Yuan, P., Leonetti, M. D., Pico, A. R., Hsiung, Y. & MacKinnon, R. Structure of the human BK channel Ca2+-activation apparatus at 3.0 Å resolution. Science 329, 182–186 (2010)

    Article  ADS  CAS  Google Scholar 

  27. Garg, P., Gardner, A., Garg, V. & Sanguinetti, M. C. Structural basis of ion permeation gating in Slo2.1 K+ channels. J. Gen. Physiol. 142, 523–542 (2013)

    Article  CAS  Google Scholar 

  28. Wilkens, C. M. & Aldrich, R. W. State-independent block of BK channels by an intracellular quaternary ammonium. J. Gen. Physiol. 128, 347–364 (2006)

    Article  CAS  Google Scholar 

  29. Zhou, Y., Xia, X. M. & Lingle, C. J. Cysteine scanning and modification reveal major differences between BK channels and Kv channels in the inner pore region. Proc. Natl Acad. Sci. USA 108, 12161–12166 (2011)

    Article  ADS  CAS  Google Scholar 

  30. 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  Google Scholar 

  31. Zhou, Y., Morais-Cabral, J. H., Kaufman, A. & MacKinnon, R. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution. Nature 414, 43–48 (2001)

    Article  ADS  CAS  Google Scholar 

  32. Joiner, W. J. et al. Formation of intermediate-conductance calcium-activated potassium channels by interaction of Slack and Slo subunits. Nature Neurosci. 1, 462–469 (1998)

    Article  CAS  Google Scholar 

  33. Zhang, X., Zeng, X. & Lingle, C. J. Slo3 K+ channels: voltage and pH dependence of macroscopic currents. J. Gen. Physiol. 128, 317–336 (2006)

    Article  CAS  Google Scholar 

  34. Dai, L., Garg, V. & Sanguinetti, M. C. Activation of Slo2.1 channels by niflumic acid. J. Gen. Physiol. 135, 275–295 (2010)

    Article  CAS  Google Scholar 

  35. 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  Google Scholar 

  36. Tao, X., Avalos, J. L., Chen, J. & MacKinnon, R. Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2 at 3.1 Å resolution. Science 326, 1668–1674 (2009)

    Article  ADS  CAS  Google Scholar 

  37. Whorton, M. R. & MacKinnon, R. Crystal structure of the mammalian GIRK2 K+ channel and gating regulation by G proteins, PIP2, and sodium. Cell 147, 199–208 (2011)

    Article  CAS  Google Scholar 

  38. Guo, D. & Lu, Z. Interaction mechanisms between polyamines and IRK1 inward rectifier K+ channels. J. Gen. Physiol. 122, 485–500 (2003)

    Article  CAS  Google Scholar 

  39. Heginbotham, L. & MacKinnon, R. Conduction properties of the cloned Shaker K+ channel. Biophys. J. 65, 2089–2096 (1993)

    Article  ADS  CAS  Google Scholar 

  40. Budelli, G., Geng, Y., Butler, A., Magleby, K. L. & Salkoff, L. Properties of Slo1 K+ channels with and without the gating ring. Proc. Natl Acad. Sci. USA 110, 16657–16662 (2013)

    Article  ADS  CAS  Google Scholar 

  41. Leonetti, M. D., Yuan, P., Hsiung, Y. & Mackinnon, R. Functional and structural analysis of the human SLO3 pH- and voltage-gated K+ channel. Proc. Natl Acad. Sci. USA 109, 19274–19279 (2012)

    Article  ADS  CAS  Google Scholar 

  42. Zhang, Z., Rosenhouse-Dantsker, A., Tang, Q. Y., Noskov, S. & Logothetis, D. E. The RCK2 domain uses a coordination site present in Kir channels to confer sodium sensitivity to Slo2.2 channels. J. Neurosci. 30, 7554–7562 (2010)

    Article  CAS  Google Scholar 

  43. Jiang, Y. et al. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417, 515–522 (2002)

    Article  ADS  CAS  Google Scholar 

  44. Thomson, S. J., Hansen, A. & Sanguinetti, M. C. Identification of the intracellular Na+ sensor in Slo2.1 potassium channels. J. Biol. Chem. 290, 14528–14535 (2015)

    Article  CAS  Google Scholar 

  45. Yang, H. et al. Activation of Slo1 BK channels by Mg2+ coordinated between the voltage sensor and RCK1 domains. Nature Struct. Mol. Biol. 15, 1152–1159 (2008)

    Article  CAS  Google Scholar 

  46. 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 

  47. Webster, S. M., Del Camino, D., Dekker, J. P. & Yellen, G. Intracellular gate opening in Shaker K+ channels defined by high-affinity metal bridges. Nature 428, 864–868 (2004)

    Article  ADS  CAS  Google Scholar 

  48. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005)

    Article  Google Scholar 

  49. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nature Methods 10, 584–590 (2013)

    Article  CAS  Google Scholar 

  50. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999)

    Article  CAS  Google Scholar 

  51. Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012)

    Article  CAS  Google Scholar 

  52. Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003)

    Article  Google Scholar 

  53. Penczek, P. A. et al. CTER-rapid estimation of CTF parameters with error assessment. Ultramicroscopy 140, 9–19 (2014)

    Article  CAS  Google Scholar 

  54. Yang, Z., Fang, J., Chittuluru, J., Asturias, F. J. & Penczek, P. A. Iterative stable alignment and clustering of 2D transmission electron microscope images. Structure 20, 237–247 (2012)

    Article  CAS  Google Scholar 

  55. Hohn, M. et al. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 157, 47–55 (2007)

    Article  CAS  Google Scholar 

  56. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)

    Article  CAS  Google Scholar 

  57. Scheres, S. H. Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 3, e03665 (2014)

    Article  Google Scholar 

  58. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003)

    Article  CAS  Google Scholar 

  59. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nature Methods 11, 63–65 (2014)

    Article  CAS  Google Scholar 

  60. Lyumkis, D., Brilot, A. F., Theobald, D. L. & Grigorieff, N. Likelihood-based classification of cryo-EM images using FREALIGN. J. Struct. Biol. 183, 377–388 (2013)

    Article  CAS  Google Scholar 

  61. Amunts, A. et al. Structure of the yeast mitochondrial large ribosomal subunit. Science 343, 1485–1489 (2014)

    Article  ADS  CAS  Google Scholar 

  62. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  63. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011)

    Article  CAS  Google Scholar 

  64. Adams, P. D. et al. The Phenix software for automated determination of macromolecular structures. Methods 55, 94–106 (2011)

    Article  CAS  Google Scholar 

  65. Ho, B. K. & Gruswitz, F. HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures. BMC Struct. Biol. 8, 49 (2008)

    Article  Google Scholar 

  66. Dolinsky, T. J. et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35, W522–W525 (2007)

    Article  Google Scholar 

  67. 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  Google Scholar 

  68. Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013)

    Article  Google Scholar 

  69. Schmidt, D., Jiang, Q. X. & MacKinnon, R. Phospholipids and the origin of cationic gating charges in voltage sensors. Nature 444, 775–779 (2006)

    Article  ADS  CAS  Google Scholar 

  70. Miller, C. (ed.) Ion Channel Reconstitution (Plenum, 1986)

    Book  Google Scholar 

  71. Ruta, V., Jiang, Y., Lee, A., Chen, J. & MacKinnon, R. Functional analysis of an archaebacterial voltage-dependent K+ channel. Nature 422, 180–185 (2003)

    Article  ADS  CAS  Google Scholar 

  72. Drozdetskiy, A., Cole, C., Procter, J. & Barton, G. J. JPred4: a protein secondary structure prediction server. Nucleic Acids Res. 43, W389–W394 (2015)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Z. Yu and J. de la Cruz at the Howard Hughes Medical Institute Janelia Cryo-EM facility for assistance in data collection, S. Harrison and S. Jenni for assistance with Phenix refinement of cryo-EM density maps, and members of the MacKinnon laboratory for discussions. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575. This work was supported in part by GM43949. R.K.H. is a Howard Hughes Medical Institute postdoctoral fellow of the Helen Hay Whitney Foundation and T.W. and R.M. are investigators of the Howard Hughes Medical Institute.

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Contributions

R.K.H. performed the experiments. P.Y. provided assistance with protein expression and purification. Z.L. aided with sample preparation and data collection. Y.H. provided assistance with protein expression. T.W. aided with initial model generation and map interpretation. R.K.H and R.M. designed the experiments and analysed the results. R.K.H. and R.M. prepared the manuscript with input from all co-authors.

Corresponding author

Correspondence to Roderick MacKinnon.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Sequence alignment of Slo channels.

a, Sequence alignment of chicken Slo2.2 with human Slo2.2 and human Slo2.1. b, Predicted position of transmembrane helices in Slo2.2 S1–S4 domain on the basis of hydropothy analysis using Jpred 4 (ref. 72). c, d, Structure-based sequence alignment of chicken Slo2.2 TMD with rat Kv chimaera (c) and chicken Slo2.2 gating ring with human Slo1 gating ring (d). Helices are blue and β-strands are red.

Extended Data Figure 2 Full channel 3D reconstruction of chicken Slo2.2.

a, Representative micrograph of detergent- and lipid-solubilized Slo2.2 in vitreous ice. b, Selected 2D class averages. c, Ab initio model of Slo2.2. d, FSC curve of the full channel reconstruction with the nominal resolution estimated to be 4.5 Å on the basis of the FSC = 0.143 (dashed line) cut-off criterion.

Extended Data Figure 3 Focused refinement of the gating ring and the TMD.

a, 3D density map of the full channel reconstruction, coloured according to local resolution (in ångströms). b, c, 3D density map calculated following focused refinement using a mask to only include the gating ring (b) and the TMD (c), coloured according to local resolution (in ångströms). d, FSC of the full channel reconstruction (estimated resolution of 4.5 Å), the gating-ring-focused refinement reconstruction (4.2 Å) and the TMD-focused refinement reconstruction (5.2 Å).

Extended Data Figure 4 Validation of the Slo2.2 model.

a, Refinement statistics for the Slo2.2 full channel, TMD and gating-ring models. b, c, FSC curves for cross-validation of the refined gating ring (b) and TMD (c) models. The black curves are the refined model compared to the full data set, the red curves are the refined model compared to half map 1 (used during test refinement) and the blue curves are the refined model compared to half map 2 (not used during test refinement).

Extended Data Figure 5 K+ ions in Slo2.2.

a, Central section of the density maps of the two independently calculated half maps (coloured in green and red) with densities corresponding to K+ ions labelled. b, Superposition of the Slo2.2 selectivity filter (green) with KcsA (PDB code 1K4C) selectivity filter (yellow). Density peaks resolved in the Slo2.2 selectivity filter at 6.5 σ are shown as blue meshes. K+ ions resolved in KcsA are shown as grey spheres.

Extended Data Figure 6 Representative segments of the cryo-EM density map.

ad, Selected regions of the gating-ring density (a, b) and the TMD density (c, d) maps with the refined model.

Extended Data Figure 7 Single channel conductance of Slo2.2.

a, Single channel current–voltage relationship (mean ± s.e.m.) for Slo2.2 in planar lipid bilayers. Single channel conductance is about 200 pS. b, Representative recordings of Slo2.2 held at −80 mV, −40 mV and 0 mV in planar lipid bilayers. Chamber solution contained 135 mM NaCl and 15 mM KCl, and cup solution contained 150 mM KCl. c, Histogram of Slo2.2 currents when held at −80 mV, −40 mV and 0 mV, as labelled.

Extended Data Figure 8 Inner helix gate.

a, Ribbon diagram of the Slo2.2 pore with Met333 side chains modelled as spheres. b, Pore radius plot as a function of distance from the extracellular surface for Slo2.2 with Met333 modelled as each of the six most frequently observed rotamers, as labelled. For distances less than about 40 Å, the curves coincide.

Extended Data Figure 9 Slo2.2 gating ring is in a closed conformation.

Wire diagrams of Slo1 gating ring in the open (top left) and closed (top right) conformations. The mobile RCK1 N lobe is black and the rest of the gating ring is grey. The N-terminal residue of the gating ring, Lys343, is shown as a pink sphere. Wire diagram of the Slo2.2 gating ring (bottom) with the RCK1 N-lobe blue and the rest of the gating ring light blue. The N-terminal residue of the gating ring, Lys351, is shown as a pink sphere.

Extended Data Table 1 3D reconstructions of chicken Slo2.2 by cryo-EM

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Hite, R., Yuan, P., Li, Z. et al. Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel. Nature 527, 198–203 (2015). https://doi.org/10.1038/nature14958

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