An online resource for GPCR structure determination and analysis

Abstract

G-protein-coupled receptors (GPCRs) transduce physiological and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb (http://www.gpcrdb.org) to assist users in designing constructs and browsing appropriate experimental conditions for structure studies.

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Fig. 1: Progress and space yet to be covered in the structural characterization of GPCRs.
Fig. 2: Snapshots from the online resource for GPCR crystallography and cryo-EM.
Fig. 3: Common GPCR structure construct modifications and alignment of constructs for structural determination.
Fig. 4: Active-state GPCR structures, including complexed proteins and cryo-EM structures.
Fig. 5: Mapping of fusion proteins and fusion sites in all GPCR structure constructs.
Fig. 6: Substitution frequencies, structural mapping and rationale for stabilizing mutations.
Fig. 7: Key expression, purification and structure determination methods and reagents.

References

  1. 1.

    Hauser, A. S., Attwood, M. M., Rask-Andersen, M., Schiöth, H. B. & Gloriam, D. E. Trends in GPCR drug discovery: new agents, targets and indications. Nat. Rev. Drug Discov. 16, 829–842 (2017). Landmark reference for GPCR drugs, targets and indications, describing recent drug discovery successes and new strategies in clinical trials.

    CAS  Article  Google Scholar 

  2. 2.

    Anonymous. Structure statistics. GPCRdb http://gpcrdb.org/structure/statistics (2018).

  3. 3.

    Rasmussen, S. G. et al. Crystal structure of the β2 adrenergic receptor–Gs protein complex. Nature 477, 549–555 (2011).

    CAS  Article  Google Scholar 

  4. 4.

    Liang, Y. L. et al. Phase-plate cryo-EM structure of a class B GPCR–G-protein complex. Nature 546, 118–123 (2017).

    CAS  Article  Google Scholar 

  5. 5.

    Koehl, A. et al. Structure of the µ-opioid receptor–Gi protein complex. Nature 558, 547–552 (2018).

    CAS  Article  Google Scholar 

  6. 6.

    Kang, Y. et al. Cryo-EM structure of human rhodopsin bound to an inhibitory G protein. Nature 558, 553–558 (2018).

    CAS  Article  Google Scholar 

  7. 7.

    Kang, Y. et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523, 561–567 (2015).

    CAS  Article  Google Scholar 

  8. 8.

    Tautermann, C. S. & Gloriam, D. E. Editorial overview: New technologies: GPCR drug design and function—exploiting the current (of) structures. Curr. Opin. Pharmacol. 30, vii–x (2016).

    CAS  Article  Google Scholar 

  9. 9.

    Manglik, A. et al. Structural insights into the dynamic process of β2-adrenergic receptor signaling. Cell 161, 1101–1111 (2015).

    CAS  Article  Google Scholar 

  10. 10.

    Van Eps, N. et al. Conformational equilibria of light-activated rhodopsin in nanodiscs. Proc. Natl Acad. Sci. USA 114, E3268–E3275 (2017).

    Article  Google Scholar 

  11. 11.

    Staus, D. P. et al. Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation. Nature 535, 448–452 (2016).

    CAS  Article  Google Scholar 

  12. 12.

    Ye, L., Van Eps, N., Zimmer, M., Ernst, O. P. & Prosser, R. S. Activation of the A2A adenosine G-protein-coupled receptor by conformational selection. Nature 533, 265–268 (2016).

    CAS  Article  Google Scholar 

  13. 13.

    Van Eps, N. et al. Gi- and Gs-coupled GPCRs show different modes of G-protein binding. Proc. Natl Acad. Sci. USA 115, 2383–2388 (2018).

    Article  Google Scholar 

  14. 14.

    Violin, J. D., Crombie, A. L., Soergel, D. G. & Lark, M. W. Biased ligands at G-protein-coupled receptors: promise and progress. Trends Pharmacol. Sci. 35, 308–316 (2014).

    CAS  Article  Google Scholar 

  15. 15.

    Congreve, M., Oswald, C. & Marshall, F. H. Applying structure-based drug design approaches to allosteric modulators of GPCRs. Trends Pharmacol. Sci. 38, 837–847 (2017).

    CAS  Article  Google Scholar 

  16. 16.

    Munk, C., Harpsøe, K., Hauser, A. S., Isberg, V. & Gloriam, D. E. Integrating structural and mutagenesis data to elucidate GPCR ligand binding. Curr. Opin. Pharmacol. 30, 51–58 (2016).

    CAS  Article  Google Scholar 

  17. 17.

    Isberg, V. et al. GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 44, D356–D364 (2016).

    CAS  Article  Google Scholar 

  18. 18.

    Isberg, V. et al. GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 42, D422–D425 (2014).

    CAS  Article  Google Scholar 

  19. 19.

    Flock, T. et al. Selectivity determinants of GPCR–G-protein binding. Nature 545, 317–322 (2017).

    CAS  Article  Google Scholar 

  20. 20.

    Pándy-Szekeres, G. et al. GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res. 46, D440–D446 (2018).

    Article  Google Scholar 

  21. 21.

    Munk, C. et al. GPCRdb: the G protein-coupled receptor database—an introduction. Br. J. Pharmacol. 173, 2195–2207 (2016).

    CAS  Article  Google Scholar 

  22. 22.

    Rose, P. W. et al. The RCSB Protein Data Bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 45, D271–D281 (2017).

    CAS  Article  Google Scholar 

  23. 23.

    Velankar, S. et al. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 41, D483–D489 (2013). Resource for residue-level mapping of UniProt (protein) and PDB (structure) entries that also integrates annotations from many more major databases.

    CAS  Article  Google Scholar 

  24. 24.

    Anonymous. Construct alignments. GPCRdb http://gpcrdb.org/construct/ (2018).

  25. 25.

    Hutchings, C. J., Koglin, M., Olson, W. C. & Marshall, F. H. Opportunities for therapeutic antibodies directed at G-protein-coupled receptors. Nat. Rev. Drug Discov. 16, 787–810 (2017).

    CAS  Article  Google Scholar 

  26. 26.

    Anonymous. Structure. GPCRdb http://gpcrdb.org/structure (2018).

  27. 27.

    Renaud, J. P. et al. Cryo-EM in drug discovery: achievements, limitations and prospects. Nat. Rev. Drug Discov. 17, 471–492 (2018). Reviews the recent advances in cryo-EM and provides an outlook of what to expect in the near future.

    CAS  Article  Google Scholar 

  28. 28.

    García-Nafría, J., Lee, Y., Bai, X., Carpenter, B. & Tate, C. G. Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein. eLife 7, e35946 (2018).

    Article  Google Scholar 

  29. 29.

    Su, X. et al. Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex. Science 357, 815–820 (2017).

    CAS  Article  Google Scholar 

  30. 30.

    Liang, Y. L. et al. Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor–Gs complex. Nature 555, 121–125 (2018).

    CAS  Article  Google Scholar 

  31. 31.

    Khoshouei, M., Radjainia, M., Baumeister, W. & Danev, R. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate. Nat. Commun. 8, 16099 (2017).

    CAS  Article  Google Scholar 

  32. 32.

    Zhang, Y. et al. Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein. Nature 546, 248–253 (2017).

    CAS  Article  Google Scholar 

  33. 33.

    Draper-Joyce, C. J. et al. Structure of the adenosine-bound human adenosine A1 receptor–Gi complex. Nature 558, 559–563 (2018).

    CAS  Article  Google Scholar 

  34. 34.

    Tsai, C. J. et al. Crystal structure of rhodopsin in complex with a mini-Go sheds light on the principles of G protein selectivity. Sci. Adv. 4, eaat7052 (2018).

    Article  Google Scholar 

  35. 35.

    García-Nafría, J., Nehmé, R., Edwards, P. C. & Tate, C. G. Cryo-EM structure of the serotonin 5-HT1B receptor coupled to heterotrimeric Go. Nature 558, 620–623 (2018).

    Article  Google Scholar 

  36. 36.

    Chun, E. et al. Fusion partner toolchest for the stabilization and crystallization of G protein-coupled receptors. Structure 20, 967–976 (2012).

    CAS  Article  Google Scholar 

  37. 37.

    Anonymous. Fusion construct analysis. GPCRdb http://gpcrdb.org/construct/analysis#fusions (2018).

  38. 38.

    Isberg, V. et al. Generic GPCR residue numbers—aligning topology maps while minding the gaps. Trends Pharmacol. Sci. 36, 22–31 (2015). Generic numbering of receptor residues crucial for all GPCR structure–function studies.

    CAS  Article  Google Scholar 

  39. 39.

    Anonymous. Mutation construct analysis. GPCRdb http://gpcrdb.org/construct/analysis#mutations (2018).

  40. 40.

    Pace, C. N. & Scholtz, J. M. A helix propensity scale based on experimental studies of peptides and proteins. Biophys. J. 75, 422–427 (1998).

    CAS  Article  Google Scholar 

  41. 41.

    Jazayeri, A. et al. Crystal structure of the GLP-1 receptor bound to a peptide agonist. Nature 546, 254–258 (2017).

    CAS  Article  Google Scholar 

  42. 42.

    Venkatakrishnan, A. J. et al. Molecular signatures of G-protein-coupled receptors. Nature 494, 185–194 (2013). Pioneering GPCR structure analysis uncovering common contact networks stabilizing the receptor fold, and characteristic features of ligand binding and receptor activation.

    CAS  Article  Google Scholar 

  43. 43.

    Anonymous. Stabilising Mutation Analyser. GPCRdb http://gpcrdb.org/construct/stabilisation (2018).

  44. 44.

    Roth, C. B., Hanson, M. A. & Stevens, R. C. Stabilization of the human β2-adrenergic receptor TM4-TM3-TM5 helix interface by mutagenesis of Glu122(3.41), a critical residue in GPCR structure. J. Mol. Biol. 376, 1305–1319 (2008).

    CAS  Article  Google Scholar 

  45. 45.

    White, K. L. et al. Structural connection between activation microswitch and allosteric sodium site in GPCR signaling. Structure 26, 259–269 (2018).

    CAS  Article  Google Scholar 

  46. 46.

    Nygaard, R., Frimurer, T. M., Holst, B., Rosenkilde, M. M. & Schwartz, T. W. Ligand binding and micro-switches in 7TM receptor structures. Trends Pharmacol. Sci. 30, 249–259 (2009).

    CAS  Article  Google Scholar 

  47. 47.

    Katritch, V., Cherezov, V. & Stevens, R. C. Structure-function of the G protein-coupled receptor superfamily. Annu. Rev. Pharmacol. Toxicol. 53, 531–556 (2013).

    CAS  Article  Google Scholar 

  48. 48.

    Carpenter, B. & Tate, C. G. Active state structures of G protein-coupled receptors highlight the similarities and differences in the G protein and arrestin coupling interfaces. Curr. Opin. Struct. Biol. 45, 124–132 (2017).

    CAS  Article  Google Scholar 

  49. 49.

    Anonymous. Truncation analysis. GPCRdb http://gpcrdb.org/construct/analysis#truncations (2018).

  50. 50.

    Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T. & Vranken, W. F. The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Res. 42, W264–W270 (2014).

    CAS  Article  Google Scholar 

  51. 51.

    Petersen, T. N., Brunak, S., von Heijne, G. & Nielsen, H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786 (2011).

    CAS  Article  Google Scholar 

  52. 52.

    Anonymous. Mutation rules. GPCRdb http://files.gpcrdb.org/mutation_rules.html (2018).

  53. 53.

    Anonymous. Local installation. GPCRdb http://docs.gpcrdb.org/local_installation.html (2018).

  54. 54.

    Peng, Y. et al. 5-HT2C receptor structures reveal the structural basis of GPCR polypharmacology. Cell 172, 719–730 (2018).

    CAS  Article  Google Scholar 

  55. 55.

    Magnani, F., Shibata, Y., Serrano-Vega, M. J. & Tate, C. G. Co-evolving stability and conformational homogeneity of the human adenosine A2a receptor. Proc. Natl Acad. Sci. USA 105, 10744–10749 (2008).

    CAS  Article  Google Scholar 

  56. 56.

    Anonymous. Experiment Browser. GPCRdb http://gpcrdb.org/construct/experiments (2018).

  57. 57.

    Zhang, X., Stevens, R. C. & Xu, F. The importance of ligands for G protein-coupled receptor stability. Trends Biochem. Sci. 40, 79–87 (2015).

    Article  Google Scholar 

  58. 58.

    Milić, D. & Veprintsev, D. B. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front. Pharmacol. 6, 66 (2015).

    PubMed  PubMed Central  Google Scholar 

  59. 59.

    Lv, X. et al. In vitro expression and analysis of the 826 human G protein-coupled receptors. Protein Cell 7, 325–337 (2016).

    CAS  Article  Google Scholar 

  60. 60.

    Luo, P. & Baldwin, R. L. Origin of the different strengths of the (i,i+4) and (i,i+3) leucine pair interactions in helices. Biophys. Chem. 96, 103–108 (2002).

    CAS  Article  Google Scholar 

  61. 61.

    Anonymous. Mutations. GPCRdb http://gpcrdb.org/construct/mutations (2018).

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Acknowledgements

We acknowledge A. Tsolakou, D. Milic and K.S. Harpsøe for help with data annotation; I. Carson for development of the preliminary version of the Stabilising Mutation Analyser; and C.-J. Tsai for input on the description of cryo-EM construct engineering and experiments. This work was supported in part by the ERC (Starting Grant 639125 to D.E.G.), the Lundbeck Foundation (grants R163-2013-16327 and R218-2016-1266 to D.E.G.), the Swiss National Science Foundation (grant CRSII2_160805 to X.D.), the European Commisions Seventh Framework Program (FP7/2007-2013; grant 290605 (COFUND: PSI-FELLOW) to E.M.) and the COST Action CM1207 (‘GLISTEN’).

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C.M., D.E.G., J.M.B. and T.F. made the construct analyses and figures; C.M. and V.I. developed the online resources; E.M. and C.M. annotated and analyzed published experimental data; L.F.N. conducted the mutagenesis experiments; M.A.H. and R.C.S. provided critical input on the project, manuscript writing and data analysis; X.D. and D.E.G. drafted the paper; all authors commented on the drafted manuscript; D.E.G. and X.D. designed the project; and D.E.G. managed the project.

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Correspondence to Christian Munk or David E. Gloriam.

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Munk, C., Mutt, E., Isberg, V. et al. An online resource for GPCR structure determination and analysis. Nat Methods 16, 151–162 (2019). https://doi.org/10.1038/s41592-018-0302-x

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