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Pore architecture and ion sites in acid-sensing ion channels and P2X receptors


Acid-sensing ion channels are proton-activated, sodium-selective channels composed of three subunits, and are members of the superfamily of epithelial sodium channels, mechanosensitive and FMRF-amide peptide-gated ion channels. These ubiquitous eukaryotic ion channels have essential roles in biological activities as diverse as sodium homeostasis, taste and pain. Despite their crucial roles in biology and their unusual trimeric subunit stoichiometry, there is little knowledge of the structural and chemical principles underlying their ion channel architecture and ion-binding sites. Here we present the structure of a functional acid-sensing ion channel in a desensitized state at 3 Å resolution, the location and composition of the 8 Å ‘thick’ desensitization gate, and the trigonal antiprism coordination of caesium ions bound in the extracellular vestibule. Comparison of the acid-sensing ion channel structure with the ATP-gated P2X4 receptor reveals similarity in pore architecture and aqueous vestibules, suggesting that there are unanticipated yet common structural and mechanistic principles.

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Figure 1: Identification of a minimally functional chicken ASIC1 construct.
Figure 2: Structure of ASIC1mfc.
Figure 3: Vestibules and possible ion permeation pathways.
Figure 4: Cs + -binding sites.
Figure 5: ASIC and P2X receptors share a common pore architecture.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession 3HGC.


  1. 1

    Waldmann, R., Champigny, G., Bassilana, F., Heurteaux, C. & Lazdunski, M. A proton-gated cation channel involved in acid-sensing. Nature 386, 173–177 (1997)

    CAS  ADS  Article  Google Scholar 

  2. 2

    Coric, T., Zheng, D., Gerstein, M. & Canessa, C. M. Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel. J. Physiol. (Lond.) 568, 725–735 (2005)

    CAS  Article  Google Scholar 

  3. 3

    Coric, T., Passamaneck, Y. J., Zhang, P., Di Gregorio, A. & Canessa, C. M. Simple chordates exhibit a proton-independent function of acid-sensing ion channels. FASEB J. 22, 1914–1923 (2008)

    CAS  Article  Google Scholar 

  4. 4

    Kellenberger, S. & Schild, L. Epithelial sodium channel/degenerin family of ion channels: a variety of functions for a shared structure. Physiol. Rev. 82, 735–767 (2002)

    CAS  Article  Google Scholar 

  5. 5

    Hesselager, M., Timmermann, D. B. & Ahring, P. K. pH dependency and desensitization kinetics of heterologously expressed combinations of acid-sensing ion channel subunits. J. Biol. Chem. 279, 11006–11015 (2004)

    CAS  Article  Google Scholar 

  6. 6

    Jasti, J., Furukawa, H., Gonzales, E. B. & Gouaux, E. Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH. Nature 449, 316–323 (2007)

    CAS  ADS  Article  Google Scholar 

  7. 7

    Carnally, S. M. et al. Direct visualization of the trimeric structure of the ASIC1a channel, using AFM imaging. Biochem. Biophys. Res. Commun. 372, 752–755 (2008)

    CAS  Article  Google Scholar 

  8. 8

    Zha, X. M. et al. Oxidant regulated inter-subunit disulfide bond formation between ASIC1a subunits. Proc. Natl Acad. Sci. USA 106, 3573–3578 (2009)

    CAS  ADS  Article  Google Scholar 

  9. 9

    Coscoy, S., Lingueglia, E., Lazdunski, M. & Barbry, P. The Phe-Met-Arg-Phe-amide-activated sodium channel is a tetramer. J. Biol. Chem. 273, 8317–8322 (1998)

    CAS  Article  Google Scholar 

  10. 10

    Kellenberger, S., Hoffmann-Pochon, N., Gautschi, I., Schneeberger, E. & Schild, L. On the molecular basis of ion permeation in the epithelial Na+ channel. J. Gen. Physiol. 114, 13–30 (1999)

    CAS  Article  Google Scholar 

  11. 11

    Bassler, E. L., Ngo-Anh, T. J., Geisler, H. S., Ruppersberg, J. P. & Gründer, S. Molecular and functional characterization of acid-sensing ion channel (ASIC) 1b. J. Biol. Chem. 276, 33782–33787 (2001)

    CAS  Article  Google Scholar 

  12. 12

    Benos, D. J., Mandel, L. J. & Simon, S. A. Cationic selectivity and competition at the sodium entry site in frog skin. J. Gen. Physiol. 76, 233–247 (1980)

    CAS  Article  Google Scholar 

  13. 13

    Palmer, L. G. Ion selectivity of the apical membrane Na channel in the toad urinary bladder. J. Membr. Biol. 67, 91–98 (1982)

    CAS  Article  Google Scholar 

  14. 14

    Kellenberger, S., Gautschi, I. & Schild, L. A single point mutation in the pore region of the epithelial Na+ channel changes ion selectivity by modifying molecular sieving. Proc. Natl Acad. Sci. USA 96, 4170–4175 (1999)

    CAS  ADS  Article  Google Scholar 

  15. 15

    Snyder, P. M., Olson, D. R. & Bucher, D. B. A pore segment in DEG/ENaC Na+ channels. J. Biol. Chem. 274, 28484–28490 (1999)

    CAS  Article  Google Scholar 

  16. 16

    Brake, A. J., Wagenbach, M. J. & Julius, D. New structural motif for ligand-gated ion channels defined by an ionotropic ATP receptor. Nature 371, 519–523 (1994)

    CAS  ADS  Article  Google Scholar 

  17. 17

    Valera, S. et al. A new class of ligand-gated ion channel defined by P2x receptor for extracellular ATP. Nature 371, 516–519 (1994)

    CAS  ADS  Article  Google Scholar 

  18. 18

    Nicke, A. et al. P2X1 and P2X3 receptors form stable trimers: a novel structural motif of ligand-gated ion channels. EMBO J. 17, 3016–3028 (1998)

    CAS  Article  Google Scholar 

  19. 19

    Aschrafi, A., Sadtler, S., Niculescu, C., Rettinger, J. & Schmalzing, G. Trimeric architecture of homomeric P2X2 and heteromeric P2X1+2 receptor subtypes. J. Mol. Biol. 342, 333–343 (2004)

    CAS  Article  Google Scholar 

  20. 20

    Surprenant, A. & North, R. A. Signaling at purinergic P2X receptors. Annu. Rev. Physiol. 71, 333–359 (2008)

    Article  Google Scholar 

  21. 21

    Kawate, T., Michel, J. C., Birdsong, W. T. & Gouaux, E. Crystal structure of the ATP-gated P2X4 ion channel in the closed state. Nature 10.1038/nature08198 (this issue)

  22. 22

    Kawate, T. & Gouaux, E. Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins. Structure 14, 673–681 (2006)

    CAS  Article  Google Scholar 

  23. 23

    Gründer, S. et al. A mutation causing pseudohypoaldosteronism type 1 identifies a conserved glycine that is involved in the gating of the epithelial sodium channel. EMBO J. 16, 899–907 (1997)

    Article  Google Scholar 

  24. 24

    Pfister, Y. et al. A gating mutation in the internal pore of ASIC1a. J. Biol. Chem. 281, 11787–11791 (2006)

    CAS  Article  Google Scholar 

  25. 25

    Dani, J. A. Ion-channel entrances influence permeation. Net charge, size, shape, and binding considerations. Biophys. J. 49, 607–618 (1986)

    CAS  ADS  Article  Google Scholar 

  26. 26

    Immke, D. C. & McCleskey, E. W. Protons open acid-sensing ion channels by catalyzing relief of Ca2+ blockade. Neuron 37, 75–84 (2003)

    CAS  Article  Google Scholar 

  27. 27

    Paukert, M., Babini, E., Pusch, M. & Gründer, S. Identification of the Ca2+ blocking site of acid-sensing ion channel (ASIC) 1: implications for channel gating. J. Gen. Physiol. 124, 383–394 (2004)

    CAS  Article  Google Scholar 

  28. 28

    Chalfie, M. & Wolinsky, E. The identification and suppression of inherited neurodegeneration in Caenorhabditis elegans . Nature 345, 410–416 (1990)

    CAS  ADS  Article  Google Scholar 

  29. 29

    Driscoll, M. & Chalfie, M. The mec-4 gene is a member of a family of Caenorhabditis elegans genes that can mutate to induce neuronal degeneration. Nature 349, 588–593 (1991)

    CAS  ADS  Article  Google Scholar 

  30. 30

    Hong, K. & Driscoll, M. A transmembrane domain of the putative channel subunit MEC-4 influences mechanotransduction and neurodegeneration in C. elegans . Nature 367, 470–473 (1994)

    CAS  ADS  Article  Google Scholar 

  31. 31

    Brown, A. L., Fernandez-Illescas, S. M., Liao, Z. & Goodman, M. B. Gain-of-function mutations in the MEC-4 DEG/ENaC sensory mechanotransduction channel alter gating and drug blockade. J. Gen. Physiol. 129, 161–173 (2007)

    CAS  Article  Google Scholar 

  32. 32

    Snyder, P. M., Bucher, D. B. & Olson, D. R. Gating induces a conformational change in the outer vestibule of ENaC. J. Gen. Physiol. 116, 781–790 (2000)

    CAS  Article  Google Scholar 

  33. 33

    Champigny, G., Voilley, N., Waldmann, R. & Lazdunski, M. Mutations causing neurodegeneration in Caenorhabditis elegans drastically alter the pH sensitivity and inactivation of the mammalian H+-gated Na+ channel MDEG1. J. Biol. Chem. 273, 15418–15422 (1998)

    CAS  Article  Google Scholar 

  34. 34

    Hille, B. Ion Channels of Excitable Membranes 3rd edn, Ch. 10 (Sinauer Associates, 2001)

    Google Scholar 

  35. 35

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

    Article  Google Scholar 

  36. 36

    Kellenberger, S., Auberson, M., Gautschi, I., Schneeberger, E. & Schild, L. Permeability properties of ENaC selectivity filter mutants. J. Gen. Physiol. 118, 679–692 (2001)

    CAS  Article  Google Scholar 

  37. 37

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

    CAS  Article  Google Scholar 

  38. 38

    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)

    CAS  ADS  Article  Google Scholar 

  39. 39

    Askwith, C. C., Benson, C. J., Welsh, M. J. & Snyder, P. M. DEG/ENaC ion channels involved in sensory transduction are modulated by cold temperature. Proc. Natl Acad. Sci. USA 98, 6459–6463 (2001)

    CAS  ADS  Article  Google Scholar 

  40. 40

    Jiang, L. H. et al. Subunit arrangement in P2X receptors. J. Neurosci. 23, 8903–8910 (2003)

    CAS  Article  Google Scholar 

  41. 41

    Silberberg, S. D., Chang, T. H. & Swartz, K. J. Secondary structure and gating rearrangements of transmembrane segments in rat P2X4 receptor channels. J. Gen. Physiol. 125, 347–359 (2005)

    CAS  Article  Google Scholar 

  42. 42

    Shaikh, S. A. & Tajkhorshid, E. Potential cation and H+ binding sites in acid sensing ion channel-1. Biophys. J. 95, 5153–5164 (2008)

    CAS  ADS  Article  Google Scholar 

  43. 43

    Cushman, K. A., Marsh-Haffner, J., Adelman, J. P. & McCleskey, E. W. A conformation change in the extracellular domain that accompanies desensitization of acid-sensing ion channel (ASIC) 3. J. Gen. Physiol. 129, 345–350 (2007)

    CAS  Article  Google Scholar 

  44. 44

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

    CAS  Article  Google Scholar 

  45. 45

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

    Article  Google Scholar 

  46. 46

    Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D. 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  47. 47

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

    Article  Google Scholar 

  48. 48

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

    CAS  Article  Google Scholar 

  49. 49

    Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–383 (2007)

    ADS  Article  Google Scholar 

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We thank the personnel at beamlines 5.0.2 of the Advanced Light Source. We also thank C. Canessa for chicken ASIC1 DNA, L. Vaskalis for assistance with illustrations, and Gouaux laboratory members for discussion. This work was supported by a National Institute of General Medical Sciences (NIGMS)-National Research Service Award (NRSA) to E.B.G. and the National Institutes of Health (NIH) (E.G.). E.G. is an investigator with the Howard Hughes Medical Institute.

Author Contributions E.G. and E.B.G. designed the project. E.B.G. performed cloning, cell culture, FSEC screening, purification, crystallography and electrophysiology. T.K. provided the zebrafish ΔP2X4 crystal structure. E.B.G. and E.G. wrote the manuscript.

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Correspondence to Eric Gouaux.

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Gonzales, E., Kawate, T. & Gouaux, E. Pore architecture and ion sites in acid-sensing ion channels and P2X receptors. Nature 460, 599–604 (2009).

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