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Cryo-EM structure of an activated GPCR–G protein complex in lipid nanodiscs

Nature Structural & Molecular Biology volume 28, pages 258–267 (2021)Cite this article

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Abstract

G-protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals. Although several structures have been solved for GPCR–G protein complexes, few are in a lipid membrane environment. Here, we report cryo-EM structures of complexes of neurotensin, neurotensin receptor 1 and Gαi1β1γ1 in two conformational states, resolved to resolutions of 4.1 and 4.2 Å. The structures, determined in a lipid bilayer without any stabilizing antibodies or nanobodies, reveal an extended network of protein–protein interactions at the GPCR–G protein interface as compared to structures obtained in detergent micelles. The findings show that the lipid membrane modulates the structure and dynamics of complex formation and provide a molecular explanation for the stronger interaction between GPCRs and G proteins in lipid bilayers. We propose an allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling.

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Fig. 1: Assembly and biophysical characterization of the NTS–NTSR1–Gαi1β1γ1 complex in cNDs.
Fig. 2: Cryo-EM structures of NTS–NTSR1–Gi–cND.
Fig. 3: Impact of the lipid bilayer on the NTSR1–Gi complex.
Fig. 4: Allosteric modulation of the GDP-binding pocket by the NTSR1–Gi interaction.
Fig. 5: Proposed mechanism of GDP release.

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Data availability

EM density maps and atomic models of the NTS–NTSR1–Gi complex in lipid nanodiscs have been deposited in the Electron Microscopy Data Bank (EMDB) and wwPDB, respectively, under accession codes EMD-23099 and PDB 7L0P (canonical state without AHD), EMD-23100 and PDB 7L0Q (canonical state with AHD), EMD-23101 and PDB 7L0R (noncanonical state without AHD) and EMD-23102 and PDB 7L0S (noncanonical state with AHD).

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Acknowledgements

Cryo-EM data were collected at the Harvard Cryo-Electron Microscopy Center for Structural Biology. We thank F. Koh, P. Egloff, P. Heine, M. Hillenbrand and J. Schöppe for their contribution to the early stages of this project; S. Sterling, R. Walsh and Z. Li for microscopy support; SBGrid for computing support; M. Deluigi for supervising the signaling experiments; and R. Walker, K. Bayer, P. Imhof and M. Bagherpoor for their advice and discussions regarding the molecular dynamics simulations. M.Z. is supported by a Charles Robert Broderick III Phytocannabinoid Research Fellowship. M.G. is supported by a Merck-BCMP fellowship. A.B. is supported by the International Retinal Research Foundation, the E. Matilda Ziegler Foundation for the Blind, the Richard and Susan Smith Family Foundation and the Pew Charitable Trusts. We acknowledge support from NIH grants GM129026 and AI037581 to G.W. and GM131401 to M.L.N. G.W. and A.P. are supported by HFSP RGP0060/2016. A.P. is supported by Swiss National Science Foundation grant no. 31003A_182334.

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Author notes

  1. These authors contributed equally: Meng Zhang, Miao Gui.

Authors and Affiliations

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

    Meng Zhang, Miao Gui, Zi-Fu Wang, Christoph Gorgulla, James J. Yu, Hao Wu, Zhen-yu J. Sun, Alan Brown & Gerhard Wagner

  2. Department of physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA

    Christoph Gorgulla

  3. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA

    Christoph Gorgulla

  4. Department of Biochemistry, University of Zurich, Zurich, Switzerland

    Christoph Klenk, Lisa Merklinger, Lena Morstein & Andreas Plückthun

  5. Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Garching, Germany

    Franz Hagn

  6. Institute of Structural Biology, Helmholtz Center Munich, Neuherberg, Germany

    Franz Hagn

  7. Department of Medicine, Division of Renal Medicine, Division of Engineering in Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Mahmoud L. Nasr

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  1. Meng Zhang
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Contributions

M.Z. developed the protocol for making NTS–NTSR1–Gαi1β1γ1–cND complexes, prepared samples, collected negative-stain EM images and performed biophysical experiments. M.G. prepared cryo-EM grids, obtained and processed the data, and built and refined the atomic models. M.Z. and Z.-F.W. performed binding experiments. C.G. performed MD simulations. J.J.Y. expressed Gαi1β1γ1. H.W. obtained and processed cryo-EM data. M.Z. and Z.-y.S. performed NMR experiments. C.K., L. Merklinger and L. Morstein made constructs and performed signaling experiments. A.P. designed and supervised the signaling experiments. F.H. and G.W. initiated the project. A.B., M.L.N. and G.W. designed and supervised the project. M.Z. wrote the manuscript. M.Z., M.G., Z.-F.W., C.G., J.J.Y., C.K., A.P., A.B., M.L.N. and G.W. edited the manuscript.

Corresponding authors

Correspondence to Alan Brown, Mahmoud L. Nasr or Gerhard Wagner.

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Competing interests

M.L.N. and G.W. founded the company NOW Scientific to sell assembled cNDs. The other authors declare no competing interests.

Additional information

Peer review information Nature Structural & Molecular Biology thanks Ka Young Chung, Arun Shukla and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Inês Chen was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Signaling competency and preparation of NTS-NTSR1-Gi complex in cNDs.

a, Signaling competency of NTSR1 constructs. Wild-type NTSR1 (50-424) or NTSR1 variants were transiently transfected into HEK293T/17 cells, and activation of Gαq signaling was quantified by measuring inositol-1-phosphate (IP1) accumulation after stimulation with NTS8–13. Data were normalized to receptor expression at the cell surface and are shown as mean and s.e.m. of n = 4 independent experiments (each performed in duplicate). Left, dose dependent IP1 production expressed as percentage of IP1 accumulation at maximal ligand concentration. Fitting of the curves result in EC50 of 2.7 nM for wild-type NTSR1 and 0.22 nM for TM86V ∆IC3B L167R. Right, bar graph showing IP1 production level at 10 µM agonist NTS8-13. The NTSR1 variant TM86V ∆IC3B lacking the L167R back mutation exhibits no IP1 production, suggesting a critical role of R1673.50 in signal transduction. b, Residues mutated in the TM86V-L167R construct shown as magenta sticks on the left and listed in the table on the right. c-e, Size-exclusion chromatograms and corresponding SDS-PAGE gels for (c) NTSR1 in DH7PC detergent micelles, (d) NTSR1 in POPC/POPG cNW9 nanodiscs before (dashed line) and after (solid line) heating, and (e) NTSR1-Gi complex in POPC/POPG cNW9 nanodiscs. f, Fractions corresponding to the NTS-NTSR1-Gi complex in (e) were analyzed by negative-stain EM, and then used for cryo-EM structure determination. Left, representative negative-stain EM micrograph of NTS-NTSR1-Gi complexes in cNDs. Right, 2D class averages.

Extended Data Fig. 2 Characterization of the binding kinetics between NTS-NTSR1 and Gi in cNDs.

a-b, Fitting of Bio-Layer Interferometry (BLI) traces of Gi binding to NTS-NTSR1-cND using (a) one binding mode and (b) two binding mode shows better fitting using two binding mode. Right, a table showing kon, koff and KD from the two binding mode fitting. c, Dissociation between Gi and NTS-NTSR1-cND in the absence (black and brown) and presence (green and blue) of GTPγS, showing faster dissociation of the complex in the presence of GTPγS, suggesting that the NTSR1-Gαi1β1γ1 complex in cNDs is capable of GDP/GTP exchange. d, Association and dissociation kinetics of Gi binding to NTS-NTSR1-cND (dark) and empty cND (gray), showing much slower association and faster dissociation of Gi binding to empty cND compared to NTS-NTSR1-cND, suggesting that interaction between Gi and NTS-NTSR1-cND is driven by Gi binding to NTSR1 rather than to the nanodisc. e, Microscale thermophoresis (MST) data for the binding between NTSR1 and Gi (square mark), as well as the binding between mutant TM86V-L167R E166A/K176A/K178A/S182A/R185A and Gi (triangle mark) in POPC/POPG (3/2) cND. f, MST data for the binding between NTSR1 and Gi in POPC cND (triangle mark), POPG cND (diamond mark) and POPC/POPG/CHS cND (square mark). Right, a table showing KD from e-f.

Extended Data Fig. 3 Cryo-EM data processing.

a, Representative micrograph showing the distribution of NTS-NTSR1-Gi-cND particles in vitreous ice. b, Selected two-dimensional class averages showing secondary structure features. The cND has an approximate diameter of 9 nm. c, Simplified flow chart of the cryo-EM processing. Two datasets were collected and processed similarly; the number of particles shown here are a conflation of both datasets. Two well-resolved classes corresponding to canonical and noncanonical states were identified. Further rounds of classification did not identify additional classes or improve the resolution or map quality. d,e, Fourier shell correlation (FSC) curves for the (d) canonical state and (e) noncanonical state with masks that either include or exclude the cND and AHD.

Extended Data Fig. 4 Cryo-EM density.

a,b, Local resolution of the NTS-NTSR1-Gi complex in the (a) canonical state and (b) noncanonical state. The local resolution was calculated in RELION-3. c,d, Density and model for the transmembrane helices of NTSR1 and the α5 and αN-helices of Gαi1 in the (c) canonical state and (d) noncanonical state. e, Density and model for NTS8-13. f, Superposition of the atomic models of NTS8-13 from the NTS-NTSR1-Gi-cND complex in the canonical (light green), and noncanonical state (dark green) with NTS from the NTS-NTSR1 crystal structure (purple; PDB 4XEE) and JMV449 (an NTS analog) from the NTSR1-Gi-detergent complex in the canonical (magenta; PDB 6OS9) and noncanonical state (dark red; PDB 6OSA).

Extended Data Fig. 5 Structure and position of the α-helical domain (AHD).

a, Density maps and models showing the interaction between Gβ1 (purple) and Gαi1 AHD (gold) in the canonical state. Zoom-in view of the Gαi1 AHD is shown. b, Density maps and models showing the interaction between Gβ1 (purple) and Gαi1 AHD (dark green) in the noncanonical state. Zoom-in view of the Gαi1 AHD is shown. The models in (a) and (b) are superposed on the Gβ1 subunits and are shown in the same view. AHD in both states interacts with the second and third blades of Gβ1. c-f, Comparison of the AHD of the canonical state NTS-NTSR1-Gi-cND (gold) with c, A crystal structure of GDP-Gi (blue; PDB 1GP2), d, A crystal structure of β2AR-Gs with nanobody Nb35 (AHD is dark red and Nb35 is green; PDB 3SN6), e, A cryo-EM structure of Rhodopsin–Gi with Fab G50 (AHD is pink and Fab G50 is green; PDB 6CMO), and f, A cryo-EM structure of Smoothened-Gi with Fab G50 (AHD is light blue and Fab G50 is green; PDB 6OT0). The models are superposed on the Gα Ras-like domain.

Extended Data Fig. 6 Cryo-EM structure of the NTS-NTSR1-Gi complex in lipid nanodiscs and the interaction with lipid.

a, Three views of the cryo-EM density map of the NTS-NTSR1-Gi-cND complex in the canonical state. b, Three views of the cryo-EM density map of the NTS-NTSR1-Gi-cND complex in the noncanonical state. The maps in panels (a) and (b) are low-pass filtered to 5 Å and colored by subunit. c, Two views of NTS-NTSR1 surrounded by nanodisc density. The transmembrane helices are shown in cylinder representation using the rainbow coloring scheme. ICL2 and helix H8 are partially submerged in lipid.

Extended Data Fig. 7 Impact of the lipid bilayer on the structure of NTSR1.

a, Comparison between the cryo-EM structures of the canonical states of NTSR1 (with Gi) in lipid bilayer (blue) and detergent (gray, PDB 6OS9). TM6 is shifted by 1.6 Å (based on Cα of V309) inwards in lipid bilayer. Right, comparison of the C-NTS-NTSR1-Gi-cND model (blue) with the density map of C-NTSR1-Gi-micelle (pink) (EMD-20180, low-pass filtered to 5 Å) confirms this shift to be significant. b, Structural comparison between the crystal structure of NTSR1 in detergent (green, PDB 4XEE) and the cryo-EM structure of the canonical state of NTSR1 in complex with Gi in detergent (gray, PDB 6OS9). The atomic models in (a) and (b) are superposed on NTSR1. c, Comparison of the localization of TM5-TM6 relative to α5-helix of Gα in class A GPCR-Gi complex structures, including the canonical state NTSR1 (blue) in complex with Gi (gold) structure reported in the current study, μOR-Gi (lime green; PDB 6DDE), Rho-Gi (hot pink; PDB 6CMO), A1R-Gi (cyan; PDB 6D9H), and CB1-Gi (purple; PDB 6N4B). The models are superposed on the Ras-like domain of Gα.

Extended Data Fig. 8 ICL2 interaction with a hydrophobic pocket of Gi.

a, Structure of GDP-Gαi showing a hydrophobic network surrounding F336 in the zoomed-in view. Residues involved in the network are shown as sticks. b, Atomic model of C-NTS-NTSR1-Gi-cND showing insertion of F17534.51 from ICL2 of NTSR1 into a hydrophobic pocket involving residues F336, L194 and V339 of Gαi. Residues involved in the network are shown as sticks. Residues from the network in (a) are shown in lines. A transition of F336 on Gαi from the network in (a) in the GDP-bound state to a new network in (b) in the NTSR1-bound state is observed.

Extended Data Fig. 9 Comparison of NTSR1-Gi interaction in lipid bilayer with detergent micelles.

a-c, Superposed structure of C-state NTSR1 (blue) and Gα (gold) in cND, NC-state NTSR1 (orchid) and Gα (dark cyan) in cND, C-state NTSR1 and Gα in micelle (gray, PDB 6OS9), NC-state NTSR1 and Gα in micelle (magenta, 6OSA). The models are superposed on NTSR1. a, extracellular view of NTSR1 and αN-helix; b, side view of NTSR1 ICL3 and α4β6 loop; c, side view of NTSR1 and α5-helix. d, Comparison of the localization of α5-helix relative to GPCR in class A GPCR-Gi complex structures, including the canonical (gold) state and noncanonical (dark cyan) state structure reported in the current study, canonical (gray) and noncanonical (magenta) state of NTSR1-Gi in detergent micelle, µOR-Gi (lime green; PDB 6DDE), A1R-Gi (cyan; PDB 6D9H), CB1-Gi (purple; PDB 6N4B), Rho-Gi (hot pink; PDB 6CMO) and DRD2–Gi (yellow; PDB 6VMS). The structures are superposed on the GPCR. Residue R3.50 is shown as colored spheres in C-state NTSR1 and as partially transparent gray spheres in the other GPCRs.

Extended Data Fig. 10 Molecular dynamics (MD) simulation for the interaction between ICL3 and the α4β6 loop.

a, MD simulation showing the salt bridges and hydrogen bonds that form between TM6-ICL3 and α4β6 loop in the canonical state of NTS-NTSR1-Gi-cND represented by simulation 12. b, Dynamics of ICL3 for each independent simulation of the canonical state of NTS-NTSR1-Gi-cND. Frames are sampled every 40 ns from each individual simulation. All 12 simulations show various interactions including salt bridges/hydrogen bonds between ICL3 and the α4β6 loop. An example of detailed interactions is shown in (a). NTSR1 is colored in blue and Gi in gold in (a,b).

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Zhang, M., Gui, M., Wang, ZF. et al. Cryo-EM structure of an activated GPCR–G protein complex in lipid nanodiscs. Nat Struct Mol Biol 28, 258–267 (2021). https://doi.org/10.1038/s41594-020-00554-6

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