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High-resolution crystal structure of human protease-activated receptor 1

Nature volume 492, pages 387–392 (2012)Cite this article

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Abstract

Protease-activated receptor 1 (PAR1) is the prototypical member of a family of G-protein-coupled receptors that mediate cellular responses to thrombin and related proteases. Thrombin irreversibly activates PAR1 by cleaving the amino-terminal exodomain of the receptor, which exposes a tethered peptide ligand that binds the heptahelical bundle of the receptor to affect G-protein activation. Here we report the 2.2-Å-resolution crystal structure of human PAR1 bound to vorapaxar, a PAR1 antagonist. The structure reveals an unusual mode of drug binding that explains how a small molecule binds virtually irreversibly to inhibit receptor activation by the tethered ligand of PAR1. In contrast to deep, solvent-exposed binding pockets observed in other peptide-activated G-protein-coupled receptors, the vorapaxar-binding pocket is superficial but has little surface exposed to the aqueous solvent. Protease-activated receptors are important targets for drug development. The structure reported here will aid the development of improved PAR1 antagonists and the discovery of antagonists to other members of this receptor family.

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Figure 1: PAR1 activation and overall structure of human PAR1 complex with antagonist vorapaxar.
Figure 2: Binding interactions of vorapaxar with human PAR1.
Figure 3: Structure motifs in PAR1 compared with other family A GPCRs.
Figure 4: Collapse of ligand-binding pocket in long-timescale molecular dynamics simulations of unliganded PAR1.
Figure 5: Residues important for agonist peptide binding and receptor activation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for PAR1 are deposited in the Protein Data Bank under accession code 3VW7.

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Acknowledgements

We acknowledge support from the National Institutes of Health, grants NS028471 (B.K.K.), and HL44907 and HL65590 (S.R.C.), and from the Mathers Foundation (B.K.K. and W.I.W.).

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Author notes

  1. Juan Jose Fung & Yaowu Zheng

    Present address: Present addresses: ProNovus Bioscience, LLC. 544 E Weddell Drive, Sunnyvale, California 94089, USA (J.J.F.); Northeast Normal University, Changchun, Jilin 130024, China (Y.Z.).,

Authors and Affiliations

  1. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, 94305, California, USA

    Cheng Zhang, Juan Jose Fung, William I. Weis & Brian K. Kobilka

  2. Cardiovascular Research Institute, University of California, San Francisco, 555 Mission Bay Boulevard South, S452P, San Francisco, California 94158, USA ,

    Yoga Srinivasan, Daniel Palmer, Yaowu Zheng & Shaun R. Coughlin

  3. D. E. Shaw Research, New York, 10036, New York, USA

    Daniel H. Arlow, Hillary F. Green, Ron O. Dror & David E. Shaw

  4. Portola Pharmaceuticals, 270 East Grand Avenue, South San Francisco, 94080, California, USA

    Anjali Pandey

  5. Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive, Stanford, 94305, California, USA

    William I. Weis

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Contributions

C.Z. optimized the construct, expressed and purified human PAR1–T4L for crystallization, developed the purification procedure, performed crystallization trials, optimized crystallization conditions, collected diffraction data, and solved and refined the structure. Y.S. helped design and make constructs for baculoviral expression, and executed and analysed cell-based functional assays of wild-type and mutant PAR1. D.H.A. designed, performed and analysed molecular dynamics simulations. J.J.F. developed the initial expression and purification protocol for PAR1. D.P. helped design, execute and analyse platelet function studies. Y.Z. helped design and make constructs for baculoviral PAR expression. H.F.G. performed and analysed molecular dynamics simulations, and assisted with manuscript preparation. A.P. made vorapaxar. R.O.D. oversaw, designed and analysed molecular dynamics simulations, and assisted with manuscript preparation. D.E.S. oversaw molecular dynamics simulations and analysis. W.I.W. assisted with X-ray diffraction data processing and crystal structure refinement. S.R.C. and B.K.K. initiated the project, planned and analysed experiments, and supervised the research and wrote the manuscript with C.Z.

Corresponding authors

Correspondence to Shaun R. Coughlin or Brian K. Kobilka.

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Zhang, C., Srinivasan, Y., Arlow, D. et al. High-resolution crystal structure of human protease-activated receptor 1. Nature 492, 387–392 (2012). https://doi.org/10.1038/nature11701

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