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Structure of an endosomal signaling GPCR–G protein–β-arrestin megacomplex

Nature Structural & Molecular Biology volume 26, pages 1123–1131 (2019)Cite this article

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Abstract

Classically, G-protein-coupled receptors (GPCRs) are thought to activate G protein from the plasma membrane and are subsequently desensitized by β-arrestin (β-arr). However, some GPCRs continue to signal through G protein from internalized compartments, mediated by a GPCR–G protein–β-arr ‘megaplex’. Nevertheless, the molecular architecture of the megaplex remains unknown. Here, we present its cryo-electron microscopy structure, which shows simultaneous engagement of human G protein and bovine β-arr to the core and phosphorylated tail, respectively, of a single active human chimeric β2-adrenergic receptor with the C-terminal tail of the arginine vasopressin type 2 receptor (β2V2R). All three components adopt their canonical active conformations, suggesting that a single megaplex GPCR is capable of simultaneously activating G protein and β-arr. Our findings provide a structural basis for GPCR-mediated sustained internalized G protein signaling.

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Fig. 1: Schematic illustration of the mechanism of sustained signaling through the formation of endosomal class B GPCR–G protein–β-arr megacomplexes.
Fig. 2: Cryo-EM structure of a β2V2R–Gs–β-arr1 megaplex.
Fig. 3: Structure and interactions of the β2V2R–Gs portion of the megaplex.
Fig. 4: Structure and interactions of the β-arr1–V2T portion of the megaplex.
Fig. 5: Comparison of the megaplex β-arr1–V2T to the V2Rpp–β-arr1–Fab30 and rhodopsin–visual arrestin crystal structures.
Fig. 6: The megaplex within a membrane environment.

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Data availability

Cryo-EM maps corresponding to the consensus megaplex reconstruction as well as the signal-subtracted β2V2R–Gs and β-arr1–V2T subcomplexes have been deposited in the Electron Microscopy Data Bank (EMDB) with accession codes EMD-9377, EMD-9376 and EMD-9375, respectively. Atomic coordinates for the β2V2R–Gs and β-arr1–V2T subcomplexes have been deposited in the Protein Data Bank (PDB) with accession codes PDB 6NI3 and PDB 6NI2, respectively. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015298. Source data for Extended Data Figs. 1c and 1d are available with the paper online. Other data that support the findings of this study are available from the corresponding authors upon request.

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Acknowledgements

We thank Q. Lennon, J. Bisson and J. Taylor for excellent administrative support, W. Capel for technical support, Y. Zhang and G. Skiniotis for help with initial sample screening, C.-R. Liang, L.-L. Gu and J.-M. Shan for synthesizing BI-167107, T. Wang and the CUNY Advanced Science Research Center Imaging Facility for help with sample screening and data collection, the lab of K. Gardner at the CUNY Advanced Science Research Center for providing various general lab reagents and equipment during initial sample screening, M. Walters, M. DeLong, M. Plue, T. Milledge, D. Capel and X. Jiang at Duke University for technical support and discussion, D. Lyumkis, D. Tegunov, W. Rice, E. Eng, L. Kim, M. Kopylov and A. Cheng for help with tilted data collection and processing and S. Houston and B. Plouffe for helpful discussion. This work received support from NIH grants (nos. T32GM007171 and F30HL149213 to A.H.N; F30HL129803 to T.J.C.; T32GM007767 to J.P.M.; R35GM133598 to A.d.G. and R01HL016037 to R.J.L.); HHMI Medical Research Fellowship to A.H.N.; the Danish Council for Independent Research & Lundbeck Foundation (DFF-5053-00136 and R172-2014-1468 to A.R.B.T.); American Heart Association Innovative Project Award (no. 19IPLOI34760706 to A.d.G); Institut de Recherche Servier (no. 18021932 to A.d.G. and D.B.-H.); and American Heart Association Predoctoral Fellowship (no. 13PRE17110027 to J.P.M.). Some of this work was performed at the Simons Electron Microscopy Center and National Resource for Automated Molecular Microscopy located at the New York Structural Biology Center, supported by grants from the Simons Foundation (grant no. SF349247), NYSTAR, and the NIH National Institute of General Medical Sciences (grant no. GM103310) with additional support from Agouron Institute (grant no. F00316) and the NIH (grant no. OD019994). R.J.L. is an HHMI Investigator.

Author information

Author notes

  1. Jacob P. Mahoney

    Present address: Department of Structural Biology, Stanford University, Stanford, CA, USA

  2. These authors contributed equally: Anthony H. Nguyen, Alex R. B. Thomsen, Thomas J. Cahill III.

Authors and Affiliations

  1. Department of Medicine, Duke University Medical Center, Durham, NC, USA

    Anthony H. Nguyen, Alex R. B. Thomsen, Thomas J. Cahill III, Li-Yin Huang, Ali Masoudi & Robert J. Lefkowitz

  2. Department of Biochemistry, Duke University Medical Center, Durham, NC, USA

    Anthony H. Nguyen, Thomas J. Cahill III, John Little IV & Robert J. Lefkowitz

  3. Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA

    Alex R. B. Thomsen

  4. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA

    Rick Huang, Chuan Hong & Zhiheng Yu

  5. Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA

    Tara Marcink

  6. Center for Host-Pathogen Interaction, Columbia University Irving Medical Center, New York, NY, USA

    Tara Marcink

  7. Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA

    Oliver B. Clarke

  8. Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA

    Oliver B. Clarke

  9. The Irving Center for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY, USA

    Oliver B. Clarke

  10. Proteomics Resource Center, The Rockefeller University, New York, NY, USA

    Søren Heissel & Henrik Molina

  11. Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA

    Danya Ben-Hail, Fadi Samaan & Amedee des Georges

  12. The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA

    Venkata P. Dandey & Yong Zi Tan

  13. Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA

    Yong Zi Tan

  14. Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA

    Jacob P. Mahoney & Roger Sunahara

  15. Structural Biology Brussels, Vrije Universiteit Brussels, Brussels, Belgium

    Sarah Triest & Jan Steyaert

  16. Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Brussels, Belgium

    Sarah Triest

  17. School of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou, China

    Xin Chen

  18. Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA

    Roger Sunahara

  19. Department of Chemistry and Biochemistry, City College of New York, New York, NY, USA

    Amedee des Georges

  20. Biochemistry and Chemistry PhD Programs, Graduate Center, City University of New York, New York, NY, USA

    Amedee des Georges

  21. Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA

    Robert J. Lefkowitz

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Contributions

A.H.N., A.R.B.T., T.J.C. III, A.d.G. and R.J.L. conceived the project and designed experimental approaches. A.H.N., A.R.B.T., T.J.C. III, L.-Y.H., A.M., J.P.M., J.L. IV and R.S. purified protein for cryo-EM structural determination. A.H.N. prepared cryo-EM samples with contributions from V.P.D. A.H.N., A.R.B.T., T.J.C. III, D.B.-H., F.S. and A.d.G. performed initial sample screenings. R.H. and Z.Y. performed cryo-EM imaging with contributions from C.H. A.H.N. processed cryo-EM data with input from A.d.G. and Y.Z.T. A.H.N. and O.B.C. built the atomic models. S.T. and J.S. raised nanobody 32 and X.C. synthesized BI-167107. S.H. and H.M. performed LC–MS/MS experiments and data analyses. T.M. performed coarse-grained molecular dynamics analysis. A.R.B.T. performed real-time cellular cAMP measurement experiments. A.H.N., A.R.B.T., T.J.C. III, A.d.G. and R.J.L. interpreted the data and wrote the manuscript. R.J.L. and A.d.G. were responsible for project supervision and management.

Corresponding authors

Correspondence to Amedee des Georges or Robert J. Lefkowitz.

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Competing interests

The authors declare no competing interests.

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Peer review information Katarzyna Marcinkiewicz was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Sample preparation and purification of the megaplex.

a, Schematic illustration of the purification and in vitro formation procedure of the megaplex. b, Size exclusion chromatogram of the precursor β2V2R–βarr1–Fab30 complex. c, SDS-PAGE gel of the β2V2R–βarr1–Fab30 complex after purification by size exclusion chromatography. d, SDS-PAGE gel of the megaplex after in vitro formation and M1 anti-Flag purification. For c-d, M denotes molecular weight (kDa) marker. Uncropped gel images for Extended Data Fig. 1c,d are provided as Source Data.

Source data

Extended Data Fig. 2 Nanobody 32 (Nb32) stabilizes the megaplex.

a, Representative micrograph and 2D class averages of megaplex samples prepared without nanobody 32 (Nb32), displaying a small percentage of megaplexes. b, Same as in a, but with a megaplex sample prepared with Nb32.

Extended Data Fig. 3 A procedure utilizing Warp and cryoSPARC for initial data processing and cleaning of one representative dataset (Dataset 2).

The same procedure was used on all dataset.

Extended Data Fig. 4

Data processing workflow for all datasets of the megaplex.

Extended Data Fig. 5 Megaplex consensus reconstruction.

a, Representative 2D class averages of the consensus megaplex reconstruction. b-c, The megaplex reconstruction is shown at high (0.115) threshold (b), and low (0.05) threshold (c). The T4L and flexible portion of the V2T appears at a lower threshold. The atomic models of the components, derived from signal subtracted reconstructions, are fitted to the consensus reconstruction. Densities for the flexible V2T and steric clash between the β2V2R and Nb32 are denoted by black circles.

Extended Data Fig. 6 Orientational distribution and resolution measurements of the megaplex.

a–d, orientational distribution (a), FSC curves indicating overall resolution (FSC = 0.143) (b), 3D-FSC to assess directional resolution anisotropy (c), and local resolution measurements (d) of the megaplex consensus reconstruction. e–j, orientational distribution (e), FSC curves indicating overall resolution (FSC = 0.143) (f), 3D-FSC to assess directional resolution anisotropy (g), map-to-model FSC and sphericity (h), local resolution measurements (i), and map-to-model FSC curve (j) of the β2V2R–Gs reconstruction. k–p, same as e–j, but for the βarr1–V2T reconstruction.

Extended Data Fig. 7 Representative densities in black mesh of various protein components.

Representative densities, from the 3.8 Å β2V2R–Gs and 4.0 Å βarr1–V2T structures, of the β2V2R, Gs subunits, and βarr1.

Extended Data Fig. 8 Representative density of the β2V2R–Gs portion of the megaplex, and comparison against other active β2AR structures.

a, Comparison of the binding pose of BI-167107 (BI) in the megaplex against three other available BI-bound β2AR structures. BI is colored green. b, Representative density showing contacts between the β2V2R and Gs in the megaplex. c, The BI binding pocket within the megaplex, accompanied by EM density for all residues within 5 Å of the ligand.

Extended Data Fig. 9 Interaction between Fab30, V2T and protein stabilizers.

a, b, Interface between βarr1 and V2T with either Nb32 (a) or Fab30 (b). Interface residues are labeled.

Extended Data Fig. 10 Verification of observed phosphorylation sites on the V2T.

a, Cryo-EM density for the six phosphorylated residues on the V2T. b, Localization probabilities of eight potential sites of phosphorylation on the V2T assessed by LC-MS/MS. A trypsin-digested fragment of the V2T is displayed. Bolded residues are phosphorylation sites observed in the cryo-EM map. Residues in red were not observed in the map, and yellow-highlighted residues were phosphorylated in both unstimulated and BI-stimulated receptors.

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Source Data Extended Data Fig. 1

Uncropped Coomassie-stained reducing SDS-PAGE gels of Extended Data Figure 1c,d.

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Nguyen, A.H., Thomsen, A.R.B., Cahill, T.J. et al. Structure of an endosomal signaling GPCR–G protein–β-arrestin megacomplex. Nat Struct Mol Biol 26, 1123–1131 (2019). https://doi.org/10.1038/s41594-019-0330-y

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