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Structural basis for σ1 receptor ligand recognition

Nature Structural & Molecular Biologyvolume 25pages981987 (2018) | Download Citation


The σ1 receptor is a poorly understood membrane protein expressed throughout the human body. Ligands targeting the σ1 receptor are in clinical trials for treatment of Alzheimer’s disease, ischemic stroke, and neuropathic pain. However, relatively little is known regarding the σ1 receptor’s molecular function. Here, we present crystal structures of human σ1 receptor bound to the antagonists haloperidol and NE-100, and the agonist (+)-pentazocine, at crystallographic resolutions of 3.1 Å, 2.9 Å, and 3.1 Å, respectively. These structures reveal a unique binding pose for the agonist. The structures and accompanying molecular dynamics (MD) simulations identify agonist-induced structural rearrangements in the receptor. Additionally, we show that ligand binding to σ1 is a multistep process that is rate limited by receptor conformational change. We used MD simulations to reconstruct a ligand binding pathway involving two major conformational changes. These data provide a framework for understanding the molecular basis for σ1 agonism.

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Atomic coordinates and crystallographic structure factors have been deposited in the Protein Data Bank under accession codes PDB 6DJZ1 receptor–haloperidol complex), PDB 6DK01 receptor–NE-100 complex), and PDB 6DK11 receptor–(+)-pentazocine complex). All other data that support the findings of this study are available from the corresponding author upon reasonable request.

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  1. 1.

    Martin, W. R., Eades, C. G., Thompson, J. A., Huppler, R. E. & Gilbert, P. E. The effects of morphine- and nalorphine- like drugs in the nondependent and morphine-dependent chronic spinal dog. J. Pharmacol. Exp. Ther. 197, 517–532 (1976).

  2. 2.

    Tam, S. W. & Cook, L. Sigma opiates and certain antipsychotic drugs mutually inhibit (+)-[3H] SKF 10,047 and [3H]haloperidol binding in guinea pig brain membranes. Proc. Natl. Acad. Sci. U.S.A. 81, 5618–5621 (1984).

  3. 3.

    Su, T. P. Evidence for sigma opioid receptor: binding of [3H]SKF-10047 to etorphine-inaccessible sites in guinea-pig brain. J. Pharmacol. Exp. Ther. 223, 284–290 (1982).

  4. 4.

    Hellewell, S. B. & Bowen, W. D. A sigma-like binding site in rat pheochromocytoma (PC12) cells: decreased affinity for (+)-benzomorphans and lower molecular weight suggest a different sigma receptor form from that of guinea pig brain. Brain Res. 527, 244–253 (1990).

  5. 5.

    Hanner, M. et al. Purification, molecular cloning, and expression of the mammalian sigma1-binding site. Proc. Natl. Acad. Sci. U.S.A. 93, 8072–8077 (1996).

  6. 6.

    Alon, A. et al. Identification of the gene that codes for the σ2 receptor. Proc. Natl. Acad. Sci. U.S.A. 114, 7160–7165 (2017).

  7. 7.

    Walker, J. M. et al. Sigma receptors: biology and function. Pharmacol. Rev. 42, 355–402 (1990).

  8. 8.

    Glennon, R. A. et al. Structural features important for sigma 1 receptor binding. J. Med. Chem. 37, 1214–1219 (1994).

  9. 9.

    Ullah, M. I. et al. In silico analysis of SIGMAR1 variant (rs4879809) segregating in a consanguineous Pakistani family showing amyotrophic lateral sclerosis without frontotemporal lobar dementia. Neurogenetics 16, 299–306 (2015).

  10. 10.

    Wong, A. Y. et al. Aberrant subcellular dynamics of Sigma-1 receptor mutants underlying neuromuscular diseases. Mol. Pharmacol. 90, 238–253 (2016).

  11. 11.

    Gregianin, E. et al. Loss-of-function mutations in the SIGMAR1 gene cause distal hereditary motor neuropathy by impairing ER-mitochondria tethering and Ca2+ signalling. Hum. Mol. Genet. 25, 3741–3753 (2016).

  12. 12.

    Hong, J. et al. Sigma-1 receptor deficiency reduces MPTP-induced parkinsonism and death of dopaminergic neurons. Cell Death Dis. 6, e1832 (2015).

  13. 13.

    Katz, J. L., Hong, W. C., Hiranita, T. & Su, T. P. A role for sigma receptors in stimulant self-administration and addiction. Behav. Pharmacol. 27, 100–115 (2016).

  14. 14.

    Castany, S., Gris, G., Vela, J. M., Verdú, E. & Boadas-Vaello, P. Critical role of sigma-1 receptors in central neuropathic pain-related behaviours after mild spinal cord injury in mice. Sci. Rep. 8, 3873 (2018).

  15. 15.

    Bruna, J. et al. Efficacy of a novel sigma-1 receptor antagonist for oxaliplatin-induced neuropathy: a randomized, double-blind, placebo-controlled phase IIa clinical trial. Neurotherapeutics 15, 178–189 (2018).

  16. 16.

    An extension study of ANAVEX2–73 in patients with mild to moderate Alzheimer’s disease (report no. NCT02756858) (Anavex Life Sciences Corp., 2018).

  17. 17.

    Urfer, R. et al. Phase II trial of the Sigma-1 receptor agonist cutamesine (SA4503) for recovery enhancement after acute ischemic stroke. Stroke 45, 3304–3310 (2014).

  18. 18.

    Kim, F. J. et al. Sigma 1 receptor modulation of G-protein-coupled receptor signaling: potentiation of opioid transduction independent from receptor binding. Mol. Pharmacol. 77, 695–703 (2010).

  19. 19.

    Navarro, G. et al. Direct involvement of sigma-1 receptors in the dopamine D1 receptor-mediated effects of cocaine. Proc. Natl. Acad. Sci. U.S.A. 107, 18676–18681 (2010).

  20. 20.

    Maurice, T. & Su, T. P. The pharmacology of sigma-1 receptors. Pharmacol. Ther. 124, 195–206 (2009).

  21. 21.

    Hayashi, T. & Su, T. P. Sigma-1 receptor chaperones at the ER-mitochondrion interface regulate Ca2+ signaling and cell survival. Cell 131, 596–610 (2007).

  22. 22.

    Aydar, E., Palmer, C. P., Klyachko, V. A. & Jackson, M. B. The sigma receptor as a ligand-regulated auxiliary potassium channel subunit. Neuron 34, 399–410 (2002).

  23. 23.

    Kourrich, S. et al. Dynamic interaction between sigma-1 receptor and Kv1.2 shapes neuronal and behavioral responses to cocaine. Cell 152, 236–247 (2013).

  24. 24.

    Hong, W. C. et al. The sigma-1 receptor modulates dopamine transporter conformation and cocaine binding and may thereby potentiate cocaine self-administration in rats. J. Biol. Chem. 292, 11250–11261 (2017).

  25. 25.

    Mishra, A. K. et al. The sigma-1 receptors are present in monomeric and oligomeric forms in living cells in the presence and absence of ligands. Biochem. J. 466, 263–271 (2015).

  26. 26.

    Gromek, K. A. et al. The oligomeric states of the purified sigma-1 receptor are stabilized by ligands. J. Biol. Chem. 289, 20333–20344 (2014).

  27. 27.

    Yano, H. et al. Pharmacological profiling of sigma 1 receptor ligands by novel receptor homomer assays. Neuropharmacology 133, 264–275 (2018).

  28. 28.

    Schmidt, H. R. et al. Crystal structure of the human σ1 receptor. Nature 532, 527–530 (2016).

  29. 29.

    Kovács, K. J. & Larson, A. A. Discrepancies in characterization of sigma sites in the mouse central nervous system. Eur. J. Pharmacol. 285, 127–134 (1995).

  30. 30.

    Bowen, W. D., de Costa, B. R., Hellewell, S. B., Walker, J. M. & Rice, K. C. [3H](+)-Pentazocine: a potent and highly selective benzomorphan-based probe for sigma-1 receptors. Mol. Neuropharmacol. 3, 117–126 (1993).

  31. 31.

    Pierce, L. C., Salomon-Ferrer, R., Augusto F de Oliveira, C., McCammon, J. A. & Walker, R. C. Routine access to millisecond time scale events with accelerated molecular dynamics. J. Chem. Theory. Comput. 8, 2997–3002 (2012).

  32. 32.

    Romero, L., Merlos, M. & Vela, J. M. Antinociception by sigma-1 receptor antagonists: central and peripheral effects. Adv. Pharmacol. 75, 179–215 (2016).

  33. 33.

    Mancuso, R. et al. Sigma-1R agonist improves motor function and motoneuron survival in ALS mice. Neurotherapeutics 9, 814–826 (2012).

  34. 34.

    Maher, C. M. et al. Small-molecule sigma1 modulator induces autophagic degradation of PD-L1. Mol. Cancer Res. 16, 243–255 (2018).

  35. 35.

    Li, D. et al. Sigma-1 receptor agonist increases axon outgrowth of hippocampal neurons via voltage-gated calcium ions channels. CNS. Neurosci. Ther. 23, 930–939 (2017).

  36. 36.

    Rosenbaum, D. M. et al. Structure and function of an irreversible agonist-β2 adrenoceptor complex. Nature 469, 236–240 (2011).

  37. 37.

    Goguadze, N., Zhuravliova, E., Morin, D., Mikeladze, D. & Maurice, T. Sigma-1 receptor agonists induce oxidative stress in mitochondria and enhance complex I activity in physiological condition but protect against pathological oxidative stress. Neurotox. Res. (2017).

  38. 38.

    Zhu, J. et al. Involvement of the delayed rectifier outward potassium channel Kv2.1 in methamphetamine-induced neuronal apoptosis via the p38 mitogen-activated protein kinase signaling pathway. J. Appl. Toxicol. 38, 696–704 (2018).

  39. 39.

    Ortíz-Rentería, M. et al. TRPV1 channels and the progesterone receptor Sig-1R interact to regulate pain. Proc. Natl. Acad. Sci. U.S.A. 115, E1657–E1666 (2018).

  40. 40.

    Kim, F. J., Schrock, J. M., Spino, C. M., Marino, J. C. & Pasternak, G. W. Inhibition of tumor cell growth by Sigma1 ligand mediated translational repression. Biochem. Biophys. Res. Commun. 426, 177–182 (2012).

  41. 41.

    Hayashi, T., Maurice, T. & Su, T. P. Ca2+ signaling via sigma(1)-receptors: novel regulatory mechanism affecting intracellular Ca2+ concentration. J. Pharmacol. Exp. Ther. 293, 788–798 (2000).

  42. 42.

    Hayashi, T. & Su, T. P. Regulating ankyrin dynamics: roles of sigma-1 receptors. Proc. Natl. Acad. Sci. U.S.A. 98, 491–496 (2001).

  43. 43.

    Kourrich, S., Su, T. P., Fujimoto, M. & Bonci, A. The sigma-1 receptor: roles in neuronal plasticity and disease. Trends Neurosci. 35, 762–771 (2012).

  44. 44.

    Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009).

  45. 45.

    Kabsch, W. Xds. Acta Crystallogr. D. Biol. Crystallogr. 66, 125–132 (2010).

  46. 46.

    Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D. Biol. Crystallogr. 69, 1204–1214 (2013).

  47. 47.

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

  48. 48.

    Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D. Biol. Crystallogr. 68, 352–367 (2012).

  49. 49.

    Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. Biol. Crystallogr. 66, 12–21 (2010).

  50. 50.

    The PyMOL Molecular Graphics System, Version 1.3r1 (Schrodinger, LLC, 2010).

  51. 51.

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

  52. 52.

    Sguazzini, E., Schmidt, H. R., Iyer, K. A., Kruse, A. C. & Dukat, M. Reevaluation of fenpropimorph as a σ receptor ligand: structure-affinity relationship studies at humanst1 receptors. Bioorg. Med. Chem. Lett. 27, 2912–2919 (2017).

  53. 53.

    Vilner, B. J., John, C. S. & Bowen, W. D. Sigma-1 and sigma-2 receptors are expressed in a wide variety of human and rodent tumor cell lines. Cancer Res. 55, 408–413 (1995).

  54. 54.

    Chu, U. B. & Ruoho, A. E. Biochemical pharmacology of the sigma-1 receptor. Mol. Pharmacol. 89, 142–153 (2016).

  55. 55.

    Linkens, K., Schmidt, H. R., Sahn, J. J., Kruse, A. C. & Martin, S. F. Investigating isoindoline, tetrahydroisoquinoline, and tetrahydrobenzazepine scaffolds for their sigma receptor binding properties. Eur. J. Med. Chem. 151, 557–567 (2018).

  56. 56.

    Friesner, R. A. et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 49, 6177–6196 (2006).

  57. 57.

    Lomize, M. A., Lomize, A. L., Pogozheva, I. D. & Mosberg, H. I. OPM: orientations of proteins in membranes database. Bioinformatics 22, 623–625 (2006).

  58. 58.

    DOWSER program (Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, 2003).

  59. 59.

    Betz, R.M. Dabble (version v.2.6.3) (2017).

  60. 60.

    Huang, J. & MacKerell, A. D. Jr. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013).

  61. 61.

    Best, R. B., Mittal, J., Feig, M. & MacKerell, A. D. Jr. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys. J. 103, 1045–1051 (2012).

  62. 62.

    Best, R. B. et al. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J. Chem. Theory. Comput. 8, 3257–3273 (2012).

  63. 63.

    Klauda, J. B. et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830–7843 (2010).

  64. 64.

    Vanommeslaeghe, K. et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31, 671–690 (2010).

  65. 65.

    Vanommeslaeghe, K. & MacKerell, A. D. Jr. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model. 52, 3144–3154 (2012).

  66. 66.

    Vanommeslaeghe, K., Raman, E. P. & MacKerell, A. D. Jr. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 52, 3155–3168 (2012).

  67. 67.

    AMBER (University of California, San Francisco, 2015).

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We thank B. Kelly for performing preliminary simulations of the σ1 receptor trimer and Advanced Photon Source GM/CA beamline staff for excellent technical support in crystallographic data collection. We also thank F. Kim (Drexel University) for generously providing (+)-pentazocine for crystallographic studies. This work was supported by a Klingenstein-Simons Fellowship in Neuroscience (A.C.K.), National Institutes of Health grants 1R01GM119185 (A.C.K.) and 1R01GM127359 (R.O.D.), the Winthrop Fund/Harvard Brain Science Initiative (A.C.K.), and National Science Foundation Graduate Research Fellowship awards DGE1745303 (H.R.S.) and DGE1656518 (R.M.B.).

Author information


  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA

    • Hayden R. Schmidt
    •  & Andrew C. Kruse
  2. Biophysics Program, Departments of Computer Science, Structural Biology, and Molecular and Cellular Physiology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA

    • Robin M. Betz
    •  & Ron O. Dror


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H.R.S. and A.C.K. designed crystallographic and pharmacological experiments. H.R.S. expressed, purified, and crystallized protein, solved crystal structures, performed radioligand binding assays, and performed Glide docking with supervision from A.C.K. R.M.B. designed, performed, and analyzed MD simulations with supervision from R.O.D. All authors interpreted results and contributed to writing of the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Andrew C. Kruse.

Integrated supplementary information

  1. Supplementary Figure 1 The structure of antagonist-bound σ1 receptor is consistent among four crystal structures.

    a, The amino acid sequence of human σ1 receptor annotated by secondary structure, based on the available crystal structures. b-e, A view of the σ1 receptor ligand binding pocket, with the protein shown in grey. All co-crystallized ligands are shown as sticks and superimposed on one another. They include PD 144418 (cyan), 4-IBP (salmon), haloperidol (orange), and NE-100 (light green)

  2. Supplementary Figure 2 Representative electron density for the crystal structures of σ1 receptor bound to haloperidol, NE-100, and ( + )-pentazocine.

    a,c,e, Composite omit 2Fo-Fc electron density contoured at 1.0σ for σ1 receptor bound to haloperidol (a), NE-100 (b), and ( + )-pentazocine (e), depicting the transmembrane domain from chain B, including residues 1–23. b,d,f, polder OMIT map around the ligand in chain C, for haloperidol (b), NE-100 (d), and ( + )-pentazocine (f) contoured at 2.0 σ

  3. Supplementary Figure 3 Analysis of the ( + )-pentazocine-bound σ1 receptor structure.

    In all panels, the σ1 receptor backbone is shown in grey cartoon, with the α4 helix shown in orange for the ( + )-pentazocine-bound structure and blue for the PD144418-bound structure. ( + )-pentazocine and PD144418 are shown in yellow and cyan sticks, respectively. a, An overall view of the ( + )-pentazocine and PD144418-bound structures aligned with once another, with red arrows indicating the direction of the α4 helix shift seen in the ( + )-pentazocine-bound structure relative to the antagonist-bound structures. b, A closeup view of the interface between the chain C and the α4 helix of chain A, highlighting the movement of Q194/C. c, a model of (-)-pentazocine (purple) superimposed on the co-crystalized ligand ( + )-pentazocine. The two ligand were aligned by the atoms outside the benzomorphan rings to illustrate that (-)-pentazocine must adopt a different pose than ( + )-pentazocine to fit into the binding pocket. d, Glide docking results for PRE-084 (green) docked into the pentazocine-bound σ1 receptor structure (PDB ID: 6DK1)

  4. Supplementary Figure 4 SPA validation and kinetic analysis of [3H]( + )-pentazocine binding.

    For all plots, error bars represent SEM, unless otherwise indication. a, Dissociation curve for [3H]( + )-pentazocine from the σ1 receptor in Sf9 membranes obtained at 37 °C. Data shown are representative of more than three independent experiments performed in triplicate. b, A time course showing total (red) and nonspecific (blue) binding of 100 nM [3H]( + )-pentazocine to σ1 receptor coupled to SPA beads. Each curve is a separate vial, with total and nonspecific binding each assayed in duplicate. c, [3H]( + )-pentazocine saturation curves for σ1 receptor binding in membranes at 37 °C (blue), and in SPA format at 23 °C (red). For the membrane binding experiment, the curve is representative of two independent experiments performed in duplicate. For the SPA measurement, the shown curve is representative of three independent experiments performed in duplicate. d, The observed rate constant for the slow step of ( + )-pentazocine association with the σ1 receptor, kslow, averaged from 3 independent association experiments performed in duplicate. For final fits, kslow was constrained to be shared for all concentrations in an independent experiment, but it is shown here unconstrained to illustrate the lack of change with concentration, which was confirmed by an ANOVA test. Error bars represent standard deviation. e, Residual plots for monophasic or biphasic decay curves for [3H]( + )-pentazocine dissociation from σ1 receptor in SPA format. Colors represent different initial concentrations of [3H]( + )-pentazocine as explained in Fig. 3a. f, The observed rate constant for the fast step of ( + )-pentazocine association with the σ1 receptor, kfast, plotted against the concentration of ( + )-pentazocine used. Values were determined from the plot shown in Fig. 3a, and are representative of three independent experiments. The solid line represents a simple exponential fit to the kfast values, to illustrate the nonlinear relationship between kfast and ( + )-pentazocine concentration. g, The observed rate constant for dissociation of [3H]( + )-pentazocine from σ1 receptor, koff, with respect to the starting concentration of ( + )-pentazocine. Values for koff were determined from the plot in Fig. 3d, and are representative of two independent experiments. h, Hill plot for σ1 receptor binding to [3H]( + )-pentazocine, generated from the saturation curve shown in b. The Hill coefficient, nH, was calculated to be 0.91 and was not significantly different than 1.0

  5. Supplementary Figure 5 SPA kinetic analysis of [3H]haloperidol binding and association of [3 H]( + )-pentazocine with σ1 receptor in membranes.

    a, Association of [3H]haloperidol with the σ1 receptor in SPA format at 23 °C. Association was measured at three concentrations: 10 nM (red), 3 nM (green), and 1 nM (blue). The black dotted lines represent the best-fit monophasic exponential association curve for each concentration, while the solid lines represent the best-fit biphasic curve. Data are representative of two independent experiments performed in duplicate. b, Residual plots for the monophasic and biphasic plots shown in a, with all colors remaining the same as in a. c, Dissociation of [3H]haloperidol from the σ1 receptor in SPA format at 23 °C. Colors denote initial [3H]haloperidol concentrations as described in a. Black lines represent the best-fit monophasic exponential decay curves for each initial concentration of ligand. d, Residual plots for monophasic or biphasic decay curves for [3H]haloperidol dissociation from σ1 receptor in SPA format. Colors represent different initial concentrations of [3H]haloperidol as explained in a. e, Association curve for 1 nM (blue circles), 10 nM (green squares), or 100 nM (red triangles) [3H]( + )-pentazocine with the σ1 receptor in Sf9 membranes obtained at 37 °C. Data shown are representative of three independent experiments performed in triplicate. The solid lines represent the best fit curves for two-step association

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