The D2 dopamine receptor (DRD2) is a therapeutic target for Parkinson’s disease1 and antipsychotic drugs2. DRD2 is activated by the endogenous neurotransmitter dopamine and synthetic agonist drugs such as bromocriptine3, leading to stimulation of Gi and inhibition of adenylyl cyclase. Here we used cryo-electron microscopy to elucidate the structure of an agonist-bound activated DRD2–Gi complex reconstituted into a phospholipid membrane. The extracellular ligand-binding site of DRD2 is remodelled in response to agonist binding, with conformational changes in extracellular loop 2, transmembrane domain 5 (TM5), TM6 and TM7, propagating to opening of the intracellular Gi-binding site. The DRD2–Gi structure represents, to our knowledge, the first experimental model of a G-protein-coupled receptor–G-protein complex embedded in a phospholipid bilayer, which serves as a benchmark to validate the interactions seen in previous detergent-bound structures. The structure also reveals interactions that are unique to the membrane-embedded complex, including helix 8 burial in the inner leaflet, ordered lysine and arginine side chains in the membrane interfacial regions, and lipid anchoring of the G protein in the membrane. Our model of the activated DRD2 will help to inform the design of subtype-selective DRD2 ligands for multiple human central nervous system disorders.
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Structural data have been deposited in the PDB with coordinate accession number 6vms, and maps have been deposited in the Electron Microscopy Data Bank (EMDB) with accession numbers EMD-21243, EMD-21244 and EMD-21245. All other data generated or analysed during this study are included in this published article or are available from the corresponding authors on reasonable request.
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Cryo-EM data were collected at the University of Texas Southwestern Medical Center Cryo-EM Facility, which is funded by the CPRIT Core Facility Support Award RP170644. We thank E. Ross for providing plasmids for G-protein expression. This project was supported by the Edward Mallinckrodt, Jr. Foundation (Scholar Award to D.M.R.), the Welch Foundation (grant I-1770 to D.M.R. and grant I-1944-20180324 to X.-c.B.), the EPFL (to P.B.), the Swiss National Science Foundation (grant 31003A_182263 to P.B.), the Ludwig Institute for Cancer research (to P.B.), the Virginia Murchison Linthicum Scholar in Medical Research at University of Texas Southwestern (to X.-c.B.), CPRIT (RR160082 to X.-c.B.) and the US National Institutes of Health (R01-GM097207 to P.B. and R01-GM083118 to R.K.S.).
P.B. is an inventor on a patent application (EP19189259.5) submitted by Ecole Polytechnique Fédérale de Lausanne on the design methods and designed protein variants herein. All other authors declare no competing interests.
Peer review information Nature thanks R. Benjamin Free, Amy Moritz, David Sibley and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data figures and tables
a, Energy landscape of three receptor variants with various energy differences in the resting (ligand-free) state ΔGresting, in the allosteric coupling controlling the inverse agonist efficacy ΔGinverse agonist and the stabilization of the receptor inactive state upon ligand stimulus. b, Active state occupancy as a function of ΔGresting and ΔGinverse agonist (the energy of inverse agonist binding), as determined by the Boltzmann law. c, Sensitivity of the receptors to inverse agonist binding. d–f, Rational design of DRD2 stabilized in the active state. DRD2 (D2) wild-type active state homology model (d). The 120-residue-long ICL3 is represented as a dotted blue line. DRD2 designed with residue microswitches shown in spheres selectively stabilizing the active state structure (e). DRD2 further stabilized in the active state through a de novo designed seven-residue stable ICL3 (f).
a, Competition binding of dopamine for [3H]spiperone on membranes containing hDRD2WT (blue) or hDRD2 modified with nT4L and de novo-designed ICL3 (nT4L-hDRD2(ΔICL3); magenta). The log-transformed inhibition constant (Ki) ± s.e.m. = −4.6 ± 0.04 for hDRD2WT. log(Ki ± s.e.m.) = −4.6 ± 0.04 for nT4L-hDRD2(ΔICL3). n = 4 biologically independent experiments on Sf9 cell membranes. b, Agonist-stimulated [35S]GTPγS binding of nT4L-hDRD2(ΔICL3) (magenta) compared to hDRD2WT (blue). Dose–responses using dopamine (closed magenta circles) or bromocriptine (BCT; open magenta circles) show log(EC50 ± s.e.m.) = −7.5 ± 0.02 and −7.8 ± 0.06, respectively, for nT4L-hDRD2(ΔICL3) compared to log(EC50 ± s.e.m.) = −7.0 ± 0.02 for dopamine on hDRD2WT (open blue circles). n = 3 biologically independent experiments on HEK293T cell membranes. c, Saturation binding of [3H]spiperone to membranes containing hDRD2WT with or without scFv16. Dissociation constant (Kd) ± s.e.m. = 0.15 ± 0.03 nM for control. Kd ± s.e.m. = 0.14 ± 0.02 nM with scFv16. n = 4 biologically independent experiments on Sf9 cell membranes. d, Competition binding of dopamine for [3H]spiperone on membranes containing DRD2WT with or without scFv16. log(Khigh ± s.e.m.) = −6.4 ± 0.3 and log(Klow ± s.e.m.) = −4.3 ± 0.08 for control. log(Khigh ± s.e.m.) = −6.5 ± 0.2 and log(Klow ± s.e.m.) = −4.3 ± 0.07 with scFv16. n = 4 biologically independent experiments on Sf9 cell membranes. In all panels, each data point is displayed as the mean with the error bars showing ± s.e.m., with individual data points for each repeat represented in small symbols.
a, Gi stimulation by dopamine in Sf9 cells transformed with Gi and hDRD2 baculoviruses. log(EC50 ± s.e.m.) = −6.3 ± 0.1 for hDRD2WT (blue). log(EC50 ± s.e.m.) = −6.6 ± 0.3 for hDRD2EM (orange). n = 4 biologically independent experiments on Sf9 cell membranes. b, Inhibition of dopamine-stimulated (10 μM) Gi activation by the inverse agonist spiperone. log( IC50 ± s.e.) = −8.6 ± 0.1 for hDRD2WT (blue). log(IC50 ± s.e.m.) = −6.3 ± 0.2 for hDRD2EM (orange). n = 4 biologically independent experiments on Sf9 cell membranes. c, Modulation of basal Gi activation by dopamine (open circles), BCT (closed circles) or spiperone (squares) with the hDRD2EM (orange symbols) relative to hDRD2WT (blue symbols). log(EC50 ± s.e.m.) for dopamine (−6.6 ± 0.2), BCT (−7.6 ± 0.1) and spiperone (−7.6 ± 0.2) for hDRD2EM. log(EC50 ± s.e.m.) for dopamine (−7.0 ± 0.1) and BCT (−7.8 ± 0.2) for hDRD2WT. n = 3 biologically independent experiments on Sf9 cell membranes. d, Apparent functional stability of agonist-bound hDRD2 constructs assessed by measuring the fraction of partially purified receptor-activating Gi as a function of incubation time at 37 °C. Half-life ± s.e.m. = 27.6 ± 1.0 min for hDRD2WT (blue). Half-life ± s.e.m. = 49.3 ± 1.1 min for hDRD2 with five designed mutations and designed truncated ICL3 (hDRD2(ΔICL3-5mut); orange). n = 3 biologically independent experiments. e, Apparent thermostability of agonist-bound hDRD2 constructs assessed by measuring the fraction of partially purified receptor-binding agonist as a function of temperature. Melting temperature (Tm) ± s.e.m. = 30.9 ± 0.9 °C for hDRD2WT (blue). Tm ± s.e.m. = 39.6 ± 0.3 °C for hDRD2(ΔICL3-5mut) (orange). n = 3 biologically independent experiments. In all panels, each data point is displayed as the mean with the error bars showing ± s.e.m., with individual data points for each repeat represented in small symbols.
a, Superose 6 gel-filtration profile of hDRD2EM–Gi-scFv16-HDL purified by M1 Flag affinity chromatography. b, Coomassie-stained PAGE of the isolated peak fraction from gel filtration. c, Overlaid Superose 200 gel-filtration profiles (in LMNG detergent) of different hDRD2 constructs purified by M1 Flag chromatography with saturating bromocriptine present. nT4L-hDRD2-5mut has the five thermostabilizing mutations of the EM construct, but has full-length ICL3. nT4L-hDRD2-ΔICL3 has the wild-type transmembrane region (no mutations) but the truncated ICL3. Receptors were purified as in Methods, but in the absence of co-transduced G-protein baculovirus.
a, Representative 2D class averages. Scale bar, 100 Å. b, Gold-standard Fourier shell correlation (FSC) curves of the 3D reconstructions. The dashed lines intercept the y axis at a FSC value of 0.143. c, Image processing procedure with the final maps coloured based on local resolution. Ctf, contrast transfer function.
Extended Data Fig. 6 3D classification with signal subtraction, model validation and representative map density.
a, Focused 3D classification subtracting T4L, the AH domain, scFv16 and rHDL/nanodisc density. b, Focused 3D classification subtracting all but the G protein. In a and b, the numbers below the images indicate the particle number in each 3D class. c, FSC curve showing the model–map correlation (focused map without T4L, the AH domain, scFv16 and rHDL/nanodisc density). The dashed line intercepts the y axis at a FSC value of 0.5. d, Representative hDRD2 transmembrane and ligand density.
Extended Data Fig. 7 Surfaces of the orthosteric pocket in the active and inactive conformations of hDRD2.
a, Solvent-accessible surface for the active conformation (purple) bound to bromocriptine (yellow sticks). b, Solvent-accessible surface for the inactive conformation (orange) bound to risperidone (green sticks), showing the deeper subpocket (PDB: 6cm4).
a, Zoomed view of the TM6–TM7 interface on the cytoplasmic side of the receptor. Atomic interactions involving the designed Y6.40 were accurately predicted in the design model. The conformation of R3.50 is displaced in the experimental structure due to the binding of Gαi, which was absent in the model. The experimental structure is in purple and the predicted DRD2 conformation is in green. b, c, Conformational energy landscape of the wild-type (b) and designed (c) DRD2 constructed from multiple all-atom MD simulation trajectories of the receptor active state homology models (orange circle) in the absence of bound agonist. The conformational space is reported along two canonical active state structure metrics (TM3–TM6 distance and NPxxY rmsd to inactive state). The DRD2 wild-type relaxes primarily due to an inactive state conformation, whereas the designed variant remains in partially active state conformation displaying large TM3–TM6 distance. The antagonist-bound DRD2 crystal structure (PDB: 6CM4) is used as a reference for the inactive state (green square).
a, AH domain density in the current structure. b, AH domain density in the rhodopsin–Gi complex (PDB: 6cmo). c, Alignment of the Gαi subunit in the hDRD2EM–Gi (purple) and the rhodopsin–Gi (blue) complexes. d, Alignment of the AH domain in the hDRD2EM–Gi (purple) and the rhodopsin–Gi (blue) complexes.
a, Surface potential of the hDRD2 (top) and Gi (bottom) components shown separately. b, Surface potential of the complex, with the scale in eV. Calculation was done using the APBS plugin in PyMOL.
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Yin, J., Chen, KY.M., Clark, M.J. et al. Structure of a D2 dopamine receptor–G-protein complex in a lipid membrane. Nature 584, 125–129 (2020). https://doi.org/10.1038/s41586-020-2379-5
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