Expression, Purification, and Structure Determination of Human PTCH1–HH-N Complexes

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Hedgehog Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2374))

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Abstract

Patched-1 (PTCH1), a tumor suppressor, serves as the receptor of Hedgehog (HH) ligand and negatively regulates the HH signaling pathway. Mutations of PTCH1 are implicated in many human cancers. Structural investigation revealed the mechanism of PTCH1-mediated HH signal regulation, further facilitating the therapeutic development of cancers. Here, we describe the expression and purification of a nearly full-length functional PTCH1 variant, PTCH1*. With purified PTCH1* protein, two forms of PTCH1*–Sonic Hedgehog (SHH) complexes were assembled, and their structures subsequently determined by cryo-electron microscope (cryo-EM).

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References

  1. Briscoe J, Therond PP (2013) The mechanisms of Hedgehog signalling and its roles in development and disease. Nat Rev Mol Cell Biol 14(7):416–429. https://doi.org/10.1038/nrm3598

    Article  CAS  PubMed  Google Scholar 

  2. Petrov K, Wierbowski BM, Salic A (2017) Sending and receiving Hedgehog signals. Annu Rev Cell Dev Biol 33:145–168. https://doi.org/10.1146/annurev-cellbio-100616-060847

    Article  CAS  PubMed  Google Scholar 

  3. Qi X, Li X (2020) Mechanistic insights into the generation and transduction of Hedgehog signaling. Trends Biochem Sci 45(5):397–410. https://doi.org/10.1016/j.tibs.2020.01.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lee JJ, Ekker SC, von Kessler DP, Porter JA, Sun BI, Beachy PA (1994) Autoproteolysis in Hedgehog protein biogenesis. Science 266(5190):1528–1537

    Article  CAS  PubMed  Google Scholar 

  5. Porter JA, Young KE, Beachy PA (1996) Cholesterol modification of hedgehog signaling proteins in animal development. Science 274(5285):255–259

    Article  CAS  PubMed  Google Scholar 

  6. Hall ET, Cleverdon ER, Ogden SK (2019) Dispatching Sonic Hedgehog: molecular mechanisms controlling deployment. Trends Cell Biol 29(5):385–395. https://doi.org/10.1016/j.tcb.2019.02.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Cannac F, Qi C, Falschlunger J, Hausmann G, Basler K, Korkhov VM (2020) Cryo-EM structure of the Hedgehog release protein dispatched. Sci Adv 6(16):eaay7928. https://doi.org/10.1126/sciadv.aay7928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen H, Liu Y, Li X (2020) Structure of human dispatched-1 provides insights into Hedgehog ligand biogenesis. Life Sci Alliance 3(8):e202000776. https://doi.org/10.26508/lsa.202000776

    Article  PubMed  PubMed Central  Google Scholar 

  9. Marigo V, Davey RA, Zuo Y, Cunningham JM, Tabin CJ (1996) Biochemical evidence that patched is the Hedgehog receptor. Nature 384(6605):176–179. https://doi.org/10.1038/384176a0

    Article  CAS  PubMed  Google Scholar 

  10. Taipale J, Cooper MK, Maiti T, Beachy PA (2002) Patched acts catalytically to suppress the activity of smoothened. Nature 418(6900):892–897. https://doi.org/10.1038/nature00989

    Article  CAS  PubMed  Google Scholar 

  11. Qi X, Liu H, Thompson B, McDonald J, Zhang C, Li X (2019) Cryo-EM structure of oxysterol-bound human smoothened coupled to a heterotrimeric Gi. Nature 571(7764):279–283. https://doi.org/10.1038/s41586-019-1286-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Deshpande I, Liang J, Hedeen D, Roberts KJ, Zhang Y, Ha B, Latorraca NR, Faust B, Dror RO, Beachy PA, Myers BR, Manglik A (2019) Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature 571(7764):284–288. https://doi.org/10.1038/s41586-019-1355-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Qi X, Friedberg L, De Bose-Boyd R, Long T, Li X (2020) Sterols in an intramolecular channel of smoothened mediate Hedgehog signaling. Nat Chem Biol 16(12):1368–1375. https://doi.org/10.1038/s41589-020-0646-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Fleet A, Lee JP, Tamachi A, Javeed I, Hamel PA (2016) Activities of the cytoplasmic domains of patched-1 modulate but are not essential for the regulation of canonical Hedgehog signaling. J Biol Chem 291(34):17557–17568. https://doi.org/10.1074/jbc.M116.731745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Qi X, Schmiege P, Coutavas E, Wang J, Li X (2018) Structures of human patched and its complex with native palmitoylated sonic hedgehog. Nature 560(7716):128–132. https://doi.org/10.1038/s41586-018-0308-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Qi X, Schmiege P, Coutavas E, Li X (2018) Two patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex. Science 362(6410):eaas8843. https://doi.org/10.1126/science.aas8843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Grant T, Grigorieff N (2015) Measuring the optimal exposure for single particle cryo-EM using a 2.6 A reconstruction of rotavirus VP6. eLife 4:e06980. https://doi.org/10.7554/eLife.06980

    Article  PubMed  PubMed Central  Google Scholar 

  18. Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10(6):584–590. https://doi.org/10.1038/nmeth.2472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Rohou A, Grigorieff N (2015) CTFFIND4: fast and accurate defocus estimation from electron micrographs. J Struct Biol 192(2):216–221. https://doi.org/10.1016/j.jsb.2015.08.008

    Article  PubMed  PubMed Central  Google Scholar 

  20. Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180(3):519–530. https://doi.org/10.1016/j.jsb.2012.09.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Grigorieff N (2016) Frealign: an exploratory tool for single-particle Cryo-EM. Methods Enzymol 579:191–226. https://doi.org/10.1016/bs.mie.2016.04.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of coot. Acta Crystallogr D Biol Crystallogr 66(Pt 4):486–501. https://doi.org/10.1107/S0907444910007493

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213–221. https://doi.org/10.1107/S0907444909052925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Brown A, Long F, Nicholls RA, Toots J, Emsley P, Murshudov G (2015) Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr 71(Pt 1):136–153. https://doi.org/10.1107/S1399004714021683

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12–21. https://doi.org/10.1107/S0907444909042073

    Article  CAS  PubMed  Google Scholar 

  26. Rubinstein JL, Brubaker MA (2015) Alignment of cryo-EM movies of individual particles by optimization of image translations. J Struct Biol 192(2):188–195. https://doi.org/10.1016/j.jsb.2015.08.007

    Article  PubMed  Google Scholar 

  27. Heymann JB, Belnap DM (2007) Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol 157(1):3–18. https://doi.org/10.1016/j.jsb.2006.06.006

    Article  CAS  PubMed  Google Scholar 

  28. Zheng SQ, Palovcak E, Armache JP, Verba KA, Cheng Y, Agard DA (2017) MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14(4):331–332. https://doi.org/10.1038/nmeth.4193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by the Endowed Scholars Program in Medical Science of UT Southwestern Medical Center and NIH grant R01 GM135343 (to X.L.). X.Q. is the recipient of a DDBrown Fellow of the Life Sciences Research Foundation. P.S. is supported by NIH grant T32 GM131963. X.L. is a Damon Runyon-Rachleff Innovator supported by the Damon Runyon Cancer Research Foundation (DRR-53-19) and a Rita C. and William P. Clements, Jr. Scholar in Biomedical Research at UT Southwestern Medical Center.

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Correspondence to **aofeng Qi or **aochun Li .

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Qi, X., Schmiege, P., Esparza, L., Li, X. (2022). Expression, Purification, and Structure Determination of Human PTCH1–HH-N Complexes. In: Li, X. (eds) Hedgehog Signaling. Methods in Molecular Biology, vol 2374. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1701-4_10

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  • DOI: https://doi.org/10.1007/978-1-0716-1701-4_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1700-7

  • Online ISBN: 978-1-0716-1701-4

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