Skip to main content

Thank you for visiting nature.com. 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.

Crystal structure of human glycine receptor-α3 bound to antagonist strychnine

Abstract

Neurotransmitter-gated ion channels of the Cys-loop receptor family are essential mediators of fast neurotransmission throughout the nervous system and are implicated in many neurological disorders. Available X-ray structures of prokaryotic and eukaryotic Cys-loop receptors provide tremendous insights into the binding of agonists, the subsequent opening of the ion channel, and the mechanism of channel activation1,2,3,4,5,6,7,8. Yet the mechanism of inactivation by antagonists remains unknown. Here we present a 3.0 Å X-ray structure of the human glycine receptor-α3 homopentamer in complex with a high affinity, high-specificity antagonist, strychnine. Our structure allows us to explore in detail the molecular recognition of antagonists. Comparisons with previous structures reveal a mechanism for antagonist-induced inactivation of Cys-loop receptors, involving an expansion of the orthosteric binding site in the extracellular domain that is coupled to closure of the ion pore in the transmembrane domain.

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.

$32.00

All prices are NET prices.

Figure 1: Architecture of the GlyRα3 bound to strychnine.
Figure 2: Orthosteric binding site occupied by the antagonist strychnine.
Figure 3: The ion channel of the GlyRα3–strychnine complex in a closed state.
Figure 4: Structural coupling at the ECD–TMD interface.
Figure 5: Conformational changes in pLGICs.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the GlyRα3–strychnine complex have been deposited in the Protein Data Bank (PDB) under accession number 5CFB.

References

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

    ADS  CAS  Article  Google Scholar 

  3. Bocquet, N. et al. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature 457, 111–114 (2009)

    ADS  CAS  Article  Google Scholar 

  4. Sauguet, L. et al. Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation. Proc. Natl Acad. Sci. USA 111, 966–971 (2014)

    ADS  CAS  Article  Google Scholar 

  5. Hibbs, R. E. & Gouaux, E. Principles of activation and permeation in an anion-selective Cys-loop receptor. Nature 474, 54–60 (2011)

    CAS  Article  Google Scholar 

  6. Miller, P. S. & Aricescu, A. R. Crystal structure of a human GABAA receptor. Nature 512, 270–275 (2014)

    ADS  CAS  Article  Google Scholar 

  7. Hassaine, G. et al. X-ray structure of the mouse serotonin 5-HT3 receptor. Nature 512, 276–281 (2014)

    ADS  CAS  Article  Google Scholar 

  8. Althoff, T., Hibbs, R. E., Banerjee, S. & Gouaux, E. X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors. Nature 512, 333–337 (2014)

    ADS  CAS  Article  Google Scholar 

  9. Legendre, P. The glycinergic inhibitory synapse. Cell. Mol. Life Sci. 58, 760–793 (2001)

    CAS  Article  Google Scholar 

  10. Lynch, J. W. Molecular structure and function of the glycine receptor chloride channel. Physiol. Rev. 84, 1051–1095 (2004)

    CAS  Article  Google Scholar 

  11. Lynch, J. W. & Callister, R. J. Glycine receptors: a new therapeutic target in pain pathways. Curr. Opin. Investig. Drugs 7, 48–53 (2006)

    CAS  PubMed  Google Scholar 

  12. Bode, A. & Lynch, J. W. The impact of human hyperekplexia mutations on glycine receptor structure and function. Mol. Brain 7, 2 (2014)

    Article  Google Scholar 

  13. Schofield, P. R. et al. Sequence and functional expression of the GABAA receptor shows a ligand-gated receptor super-family. Nature 328, 221–227 (1987)

    ADS  CAS  Article  Google Scholar 

  14. Langosch, D., Thomas, L. & Betz, H. Conserved quaternary structure of ligand-gated ion channels: the postsynaptic glycine receptor is a pentamer. Proc. Natl Acad. Sci. USA 85, 7394–7398 (1988)

    ADS  CAS  Article  Google Scholar 

  15. 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 

  16. 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 

  17. Hansen, S. B. et al. Structures of Aplysia AChBP complexes with nicotinic agonists and antagonists reveal distinctive binding interfaces and conformations. EMBO J. 24, 3635–3646 (2005)

    CAS  Article  Google Scholar 

  18. Billen, B. et al. Molecular actions of smoking cessation drugs at α4β2 nicotinic receptors defined in crystal structures of a homologous binding protein. Proc. Natl Acad. Sci. USA 109, 9173–9178 (2012)

    ADS  CAS  Article  Google Scholar 

  19. Moraga-Cid, G. et al. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proc. Natl Acad. Sci. USA 112, 2865–2870 (2015)

    ADS  CAS  Article  Google Scholar 

  20. Rajendra, S., Lynch, J. W. & Schofield, P. R. The glycine receptor. Pharmacol. Ther. 73, 121–146 (1997)

    CAS  Article  Google Scholar 

  21. Laube, B., Maksay, G., Schemm, R. & Betz, H. Modulation of glycine receptor function: a novel approach for therapeutic intervention at inhibitory synapses? Trends Pharmacol. Sci. 23, 519–527 (2002)

    CAS  Article  Google Scholar 

  22. Grenningloh, G. et al. Alpha subunit variants of the human glycine receptor: primary structures, functional expression and chromosomal localization of the corresponding genes. EMBO J. 9, 771–776 (1990)

    CAS  Article  Google Scholar 

  23. Jensen, A. A., Gharagozloo, P., Birdsall, N. J. & Zlotos, D. P. Pharmacological characterisation of strychnine and brucine analogues at glycine and α7 nicotinic acetylcholine receptors. Eur. J. Pharmacol. 539, 27–33 (2006)

    CAS  Article  Google Scholar 

  24. Mohsen, A. M., Heller, E., Holzgrabe, U., Jensen, A. A. & Zlotos, D. P. Structure–activity relationships of strychnine analogs at glycine receptors. Chem. Biodivers. 11, 1256–1262 (2014)

    CAS  Article  Google Scholar 

  25. Grudzinska, J. et al. The β subunit determines the ligand binding properties of synaptic glycine receptors. Neuron 45, 727–739 (2005)

    CAS  Article  Google Scholar 

  26. Brams, M. et al. A structural and mutagenic blueprint for molecular recognition of strychnine and d-tubocurarine by different Cys-loop receptors. PLoS Biol. 9, e1001034 (2011)

    CAS  Article  Google Scholar 

  27. Becker, C. M., Hoch, W. & Betz, H. Glycine receptor heterogeneity in rat spinal cord during postnatal development. EMBO J. 7, 3717–3726 (1988)

    CAS  Article  Google Scholar 

  28. Vandenberg, R. J., French, C. R., Barry, P. H., Shine, J. & Schofield, P. R. Antagonism of ligand-gated ion channel receptors: two domains of the glycine receptor α subunit form the strychnine-binding site. Proc. Natl Acad. Sci. USA 89, 1765–1769 (1992)

    ADS  CAS  Article  Google Scholar 

  29. Calimet, N. et al. A gating mechanism of pentameric ligand-gated ion channels. Proc. Natl Acad. Sci. USA 110, E3987–E3996 (2013)

    CAS  Article  Google Scholar 

  30. Yu, R. et al. Agonist and antagonist binding in human glycine receptors. Biochemistry 53, 6041–6051 (2014)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  32. McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D 63, 32–41 (2007)

    CAS  Article  Google Scholar 

  33. Schuttelkopf, A. W. & van Aalten, D. M. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D 60, 1355–1363 (2004)

    Article  Google Scholar 

  34. 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 

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

    Article  Google Scholar 

  36. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)

    ADS  Article  Google Scholar 

  37. 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)

    ADS  CAS  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. DeLano, W. L. The PyMOL molecular graphics system (DeLano Scientific, 2002)

    Google Scholar 

  40. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)

    CAS  Article  Google Scholar 

  41. Jensen, A. A. & Kristiansen, U. Functional characterisation of the human α1 glycine receptor in a fluorescence-based membrane potential assay. Biochem. Pharmacol. 61, 1789–1799 (2004)

    Article  Google Scholar 

Download references

Acknowledgements

We thank G. Ranieri and R. Walter at Shamrock Structures and the staff at beamlines 08-ID at the Canadian Light Source and 22-ID at the Advanced Photon Source for data collection. We are grateful to Z. Wang and J. Gingras for reviewing the manuscript.

Author information

Authors and Affiliations

Authors

Contributions

The authors have jointly contributed to project design, data analysis and manuscript preparation. P.L.S. performed initial construct design and purification experiments, structure solution, model building, and structural analysis; X.H. performed protein purifications, crystallization, model building, and structural analysis; H.C. performed cloning and expression experiments; K.M. performed SPR and ITC binding studies; S.S. performed functional testing; P.L.S. and X.H. wrote the manuscript with help from K.M., S.S., and H.C.

Corresponding authors

Correspondence to Xin Huang or Paul L. Shaffer.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Strychnine binding to GlyRα3cryst in detergent micelles.

a, Binding thermodynamics and stoichometry of strychnine to GlyRα3cryst analysed by ITC. The individual peaks from titrations are integrated and presented in a Wiseman plot. An appropriate binding model is chosen and the isotherm is then fitted to yield the binding enthalpy ΔH, the dissociation constant Kd, and the stoichiometry n. b, Binding kinetics of strychnine to GlyRα3cryst measured by SPR spectroscopy.

Extended Data Figure 2 Glycine dose–response to GlyRα3cryst in HEK293T cells.

Glycine dose–response curve for BacMam baculovirus-transduced HEK293T cells expressing either wild-type human GlyRα3 (GlyRα3, filled circles) or GlyRα3cryst (open circles) measured by membrane potential dye assay (see Methods for details). Each data point represents a value of n = 4–6 and normalized to a maximum glycine response observed at 2 mM glycine concentration. Glycine EC50 for GlyRα3 was calculated at 150 ± 10.6 µM (n = 4, 95% confidence interval) and GlyRα3cryst at 16.4 ± 1.2 µM (n = 5, 95% confidence interval).

Extended Data Figure 3 Architecture of the GlyRα3 bound to strychnine and crystallographic packing of GlyRα3cryst.

a, The GlyRα3–strychnine complex viewed from the extracellular side of the membrane down the pore axis, perpendicular to the membrane. Strychnine is bound at the interface between subunits. b, The GlyRα3–strychnine complex viewed from the intracellular side down the pore axis. The M2 helices are shown lining the pore. c, d, Packing of the GlyRα3–strychnine complex. Receptor in the asymmetric unit is coloured by subunit, with subunit A in pale green and subunit B in cyan. Strychnine molecules are shown as spheres and are coloured to match their associated principal subunit. Symmetry-related receptors are coloured grey. The interface between subunits A and B is completely exposed to solvent in the crystal lattice, and this interface was used in the making of all figures for this paper to avoid any potential crystal-packing artefacts.

Extended Data Figure 4 Strychnine binding to GlyRα3.

a, b, Two views of the strychnine-binding pocket showing 2FoFc omit electron density maps. The principal subunit is coloured pale green, the complementary subunit is cyan, and strychnine is grey. Strychnine was omitted from map calculations. Map is contoured at 1.0σ. The hydrogen bond between the backbone carbonyl of Phe159 and the tertiary nitrogen of strychnine is shown as a dotted line. c, d, Same views and representations as in a and b, but FoFc omit electron density is shown. Contour level of map is 3.0σ. e, Chemical structure of strychnine. Ring numbering is denoted by red Roman numerals. Carbon and nitrogen historic numbering conventions are denoted by blue numbers. f, Solvent-accessible surface area of the complementary side of the binding interface coloured by electrostatic potential. The complementary subunit interface has a positive electrostatic potential to interact with the partial negative charge of the lactam oxygen of strychnine.

Extended Data Figure 5 Sequence alignment of GlyRα3cryst with representative eukaryotic Cys-loop receptor family members.

Residue conservation is indicated by grey and black highlights. Site of N-linked glycosylation of GlyRα3cryst is indicated by the orange hexagon. Residues involved in binding of strychnine are indicated by green (the principal subunit) and cyan (the complementary subunit) dots. Red triangles above residues indicate mutations in GlyRα1 or GlyRβ that cause hyperekplexia. Signal peptides have been removed from all protein sequences. Secondary structure elements are denoted by cylinders (helices) and arrows (strands) above the alignment. The alignment was generated using ClustalW. Protein sequences are from the following entires: human GlyRα1 (Uniprot P23415), human GlyRβ (Uniprot 48167), GluClcryst (PDB accession number 4TNV), GABAAR-β3cryst (PDB accession number 4COF), and 5HT3A (PDB accession number 4PIR).

Extended Data Figure 6 Structural alignment of pLGICs.

a, Structures of GlyRα3cryst (green), apo-GluClα (slate), and glutamate- and ivermectin-bound GluCLα (violet) aligned using their ECDs. b, Close-up view of the loop C, rotated 45 ° clockwise along the horizontal axis (left to right) to optimize viewing. c, Close-up view of loops β6–β7 and β1–β2. d, Table showing regions of GlyRα3 used for structural alignments, as well as resulting number of overlapped Cα atoms and root mean squared deviation distances. PDB accession numbers are listed for each reference structure.

Extended Data Figure 7 Representative electron density for the ECD–TMD interface.

Final 2FoFc electron density map around the region of the ECD–TMD interface is shown, contoured at 1.0σ. Protomer A is shown in pale green, protomer B in cyan, and protomer C in magenta. Important secondary structure elements and loops are noted.

Extended Data Table 1 Crystallographic and structure refinement statistics

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Huang, X., Chen, H., Michelsen, K. et al. Crystal structure of human glycine receptor-α3 bound to antagonist strychnine. Nature 526, 277–280 (2015). https://doi.org/10.1038/nature14972

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature14972

This article is cited by

Comments

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.

Search

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