Skip to main content

Thank you for visiting 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.

Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel


The X-ray structure of a pentameric ligand-gated ion channel from Erwinia chrysanthemi (ELIC) has recently provided structural insight into this family of ion channels at high resolution1. The structure shows a homo-pentameric protein with a barrel-stave architecture that defines an ion-conduction pore located on the fivefold axis of symmetry. In this structure, the wide aqueous vestibule that is encircled by the extracellular ligand-binding domains of the five subunits narrows to a discontinuous pore that spans the lipid bilayer. The pore is constricted by bulky hydrophobic residues towards the extracellular side, which probably serve as barriers that prevent the diffusion of ions. This interrupted pore architecture in ELIC thus depicts a non-conducting conformation of a pentameric ligand-gated ion channel, the thermodynamically stable state in the absence of bound ligand. As ligand binding promotes pore opening in these ion channels and the specific ligand for ELIC has not yet been identified, we have turned our attention towards a homologous protein from the cyanobacterium Gloebacter violaceus (GLIC). GLIC was shown to form proton-gated channels that are activated by a pH decrease on the extracellular side and that do not desensitize after activation2. Both prokaryotic proteins, ELIC and GLIC form ion channels that are selective for cations over anions with poor discrimination among monovalent cations1,2, characteristics that resemble the conduction properties of the cation-selective branch of the family that includes acetylcholine and serotonin receptors3,4. Here we present the X-ray structure of GLIC at 3.1 Å resolution. The structure reveals a conformation of the channel that is distinct from ELIC and that probably resembles the open state. In combination, both structures suggest a novel gating mechanism for pentameric ligand-gated ion channels where channel opening proceeds by a change in the tilt of the pore-forming helices.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: GLIC structure.
Figure 2: Comparison of the pore region.
Figure 3: Pore structure and ion binding.
Figure 4: Extracellular domain.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates of GLIC have been deposited in the Protein Data Bank under accession number 3EHZ (WT), and 3EI0 (E221A).


  1. Hilf, R. J. & Dutzler, R. X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature 452, 375–379 (2008)

    ADS  CAS  Article  Google Scholar 

  2. Bocquet, N. et al. A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature 445, 116–119 (2007)

    ADS  CAS  Article  Google Scholar 

  3. Karlin, A. Emerging structure of the nicotinic acetylcholine receptors. Nature Rev. Neurosci. 3, 102–114 (2002)

    CAS  Article  Google Scholar 

  4. Adams, D. J., Dwyer, T. M. & Hille, B. The permeability of endplate channels to monovalent and divalent metal cations. J. Gen. Physiol. 75, 493–510 (1980)

    CAS  Article  Google Scholar 

  5. Tasneem, A., Iyer, L. M., Jakobsson, E. & Aravind, L. Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol. 6, R4 (2004)

    Article  Google Scholar 

  6. Miyazawa, A., Fujiyoshi, Y. & Unwin, N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 423, 949–955 (2003)

    ADS  CAS  Article  Google Scholar 

  7. Unwin, N. Refined structure of the nicotinic acetylcholine receptor at 4Å resolution. J. Mol. Biol. 346, 967–989 (2005)

    CAS  Article  Google Scholar 

  8. Imoto, K. et al. Rings of negatively charged amino acids determine the acetylcholine receptor channel conductance. Nature 335, 645–648 (1988)

    ADS  CAS  Article  Google Scholar 

  9. Konno, T. et al. Rings of anionic amino acids as structural determinants of ion selectivity in the acetylcholine receptor channel. Proc. R. Soc. Lond. B 244, 69–79 (1991)

    ADS  CAS  Article  Google Scholar 

  10. 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)

    ADS  CAS  Article  Google Scholar 

  11. Sine, S. M. & Engel, A. G. Recent advances in Cys-loop receptor structure and function. Nature 440, 448–455 (2006)

    ADS  CAS  Article  Google Scholar 

  12. Brejc, K. et al. Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411, 269–276 (2001)

    ADS  CAS  Article  Google Scholar 

  13. Celie, P. H. et al. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures. Neuron 41, 907–914 (2004)

    CAS  Article  Google Scholar 

  14. Lee, W. Y. & Sine, S. M. Principal pathway coupling agonist binding to channel gating in nicotinic receptors. Nature 438, 243–247 (2005)

    ADS  CAS  Article  Google Scholar 

  15. Sala, F., Mulet, J., Sala, S., Gerber, S. & Criado, M. Charged amino acids of the N-terminal domain are involved in coupling binding and gating in alpha7 nicotinic receptors. J. Biol. Chem. 280, 6642–6647 (2005)

    CAS  Article  Google Scholar 

  16. Schofield, C. M., Jenkins, A. & Harrison, N. L. A highly conserved aspartic acid residue in the signature disulfide loop of the alpha 1 subunit is a determinant of gating in the glycine receptor. J. Biol. Chem. 278, 34079–34083 (2003)

    CAS  Article  Google Scholar 

  17. Jha, A., Cadugan, D. J., Purohit, P. & Auerbach, A. Acetylcholine receptor gating at extracellular transmembrane domain interface: The cys-loop and M2–M3 linker. J. Gen. Physiol. 130, 547–558 (2007)

    CAS  Article  Google Scholar 

  18. Dani, J. A. Open channel structure and ion binding sites of the nicotinic acetylcholine receptor channel. J. Neurosci. 9, 884–892 (1989)

    CAS  Article  Google Scholar 

  19. Dani, J. A. & Eisenman, G. Monovalent and divalent cation permeation in acetylcholine receptor channels. Ion transport related to structure. J. Gen. Physiol. 89, 959–983 (1987)

    CAS  Article  Google Scholar 

  20. Galzi, J. L. et al. Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic. Nature 359, 500–505 (1992)

    ADS  CAS  Article  Google Scholar 

  21. Corringer, P. J. et al. Mutational analysis of the charge selectivity filter of the alpha7 nicotinic acetylcholine receptor. Neuron 22, 831–843 (1999)

    CAS  Article  Google Scholar 

  22. Gunthorpe, M. J. & Lummis, S. C. Conversion of the ion selectivity of the 5-HT(3a) receptor from cationic to anionic reveals a conserved feature of the ligand-gated ion channel superfamily. J. Biol. Chem. 276, 10977–10983 (2001)

    CAS  Article  Google Scholar 

  23. Pascual, J. M. & Karlin, A. State-dependent accessibility and electrostatic potential in the channel of the acetylcholine receptor. Inferences from rates of reaction of thiosulfonates with substituted cysteines in the M2 segment of the alpha subunit. J. Gen. Physiol. 111, 717–739 (1998)

    CAS  Article  Google Scholar 

  24. Wilson, G. G., Pascual, J. M., Brooijmans, N., Murray, D. & Karlin, A. The intrinsic electrostatic potential and the intermediate ring of charge in the acetylcholine receptor channel. J. Gen. Physiol. 115, 93–106 (2000)

    CAS  Article  Google Scholar 

  25. Unwin, N. Acetylcholine receptor channel imaged in the open state. Nature 373, 37–43 (1995)

    ADS  CAS  Article  Google Scholar 

  26. Paas, Y. et al. Pore conformations and gating mechanism of a Cys-loop receptor. Proc. Natl Acad. Sci. USA 102, 15877–15882 (2005)

    ADS  CAS  Article  Google Scholar 

  27. Cymes, G. D., Ni, Y. & Grosman, C. Probing ion-channel pores one proton at a time. Nature 438, 975–980 (2005)

    ADS  CAS  Article  Google Scholar 

  28. Cymes, G. D. & Grosman, C. Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer. Nature Struct. Mol. Biol. 15, 389–396 (2008)

    CAS  Article  Google Scholar 

  29. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993)

    CAS  Article  Google Scholar 

  30. Leslie, A. G. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography (No. 26, Daresbury Laboratory, 1992)

    Google Scholar 

  31. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)

    Article  Google Scholar 

  32. CCP4. Collaborative Computational Project Nr. 4. The CCP4 Suite: Programs for X-ray crystallography. Acta Crystallogr. D 50, 760–763 (1994)

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

    CAS  Article  Google Scholar 

  34. Cowtan, K. An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 34–38 (No. 31, Daresbury Laboratory, 1994)

    Google Scholar 

  35. 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  Google Scholar 

  36. 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 

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

    Article  Google Scholar 

  38. Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A. & Sansom, M. S. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 354–360, 376 (1996)

    CAS  Article  Google Scholar 

  39. Sanner, M. F., Olson, A. J. & Spehner, J. C. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38, 305–320 (1996)

    CAS  Article  Google Scholar 

  40. Brooks, B. R. et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187–217 (1983)

    CAS  Article  Google Scholar 

  41. Im, W., Beglov, D. & Roux, B. Continuum solvation model: Electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput. Phys. Commun. 111, 59–75 (1998)

    ADS  CAS  Article  Google Scholar 

  42. Lorenz, C., Pusch, M. & Jentsch, T. J. Heteromultimeric CLC chloride channels with novel properties. Proc. Natl Acad. Sci. USA 93, 13362–13366 (1996)

    ADS  CAS  Article  Google Scholar 

Download references


We thank B. Blattmann and C. Stutz-Duocommun for assistance with crystal screening, C. Schulze-Briese and the staff of the X06SA beamline for support during data collection, the protein analysis group at the functional genomics centre of the University of Zurich for help with mass spectrometry, R. MacKinnon for comments on the manuscript and members of the Dutzler laboratory for help in all stages of the project. Data collection was performed at the Swiss Light Source of the Paul Scherrer Institute. The research leading to these results was supported by a grant from the National Center for Competence in Research (NCCR) in Structural Biology and by an EC FP7 grant for the EDICT consortium (HEALTH-201924). R.J.C.H. is affiliated with the Molecular Life Sciences Ph.D. programme of the University/ETH Zurich.

Author Contributions R.D. and R.J.C.H. designed the project. R.J.C.H. carried out all experiments. R.D. assisted in data collection and structure determination. R.D. and R.J.C.H. jointly wrote the manuscript.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Raimund Dutzler.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S10 with Legends and Supplementary Tables S1 -S2. (PDF 2340 kb)

Supplementary Movie 1

Supplementary Movie 1 contains a morph of conserved parts of the Ca trace between ELIC and GLIC. The view is from the extracellular side. (MPG 1711 kb)

Supplementary Movie 2

Supplementary Movie 2 contains a morph of conserved parts of the Ca trace between ELIC and GLIC. The view is from within the membrane. (MPG 1583 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hilf, R., Dutzler, R. Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nature 457, 115–118 (2009).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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.


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