7X2D

Cryo-EM structure of the tavapadon-bound D1 dopamine receptor and mini-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ligand recognition and biased agonism of the D1 dopamine receptor.

Teng, X.Chen, S.Nie, Y.Xiao, P.Yu, X.Shao, Z.Zheng, S.

(2022) Nat Commun 13: 3186-3186

  • DOI: https://doi.org/10.1038/s41467-022-30929-w
  • Primary Citation of Related Structures:  
    7X2C, 7X2D, 7X2F

  • PubMed Abstract: 

    Dopamine receptors are widely distributed in the central nervous system and are important therapeutic targets for treatment of various psychiatric and neurological diseases. Here, we report three cryo-electron microscopy structures of the D1 dopamine receptor (D1R)-Gs complex bound to two agonists, fenoldopam and tavapadon, and a positive allosteric modulator LY3154207. The structure reveals unusual binding of two fenoldopam molecules, one to the orthosteric binding pocket (OBP) and the other to the extended binding pocket (EBP). In contrast, one elongated tavapadon molecule binds to D1R, extending from OBP to EBP. Moreover, LY3154207 stabilizes the second intracellular loop of D1R in an alpha helical conformation to efficiently engage the G protein. Through a combination of biochemical, biophysical and cellular assays, we further show that the broad conformation stabilized by two fenoldopam molecules and interaction between TM5 and the agonist are important for biased signaling of D1R.


  • Organizational Affiliation

    Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D(1A) dopamine receptorA [auth F]473Homo sapiensMutation(s): 0 
Gene Names: DRD1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21728 (Homo sapiens)
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Go to UniProtKB:  P21728
PHAROS:  P21728
GTEx:  ENSG00000184845 
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UniProt GroupP21728
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortB [auth A]248Homo sapiensMutation(s): 0 
Gene Names: GNAS
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]358Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 1 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody35160synthetic constructMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
86W (Subject of Investigation/LOI)
Query on 86W

Download Ideal Coordinates CCD File 
G [auth F]1,5-dimethyl-6-[2-methyl-4-[3-(trifluoromethyl)pyridin-2-yl]oxy-phenyl]pyrimidine-2,4-dione
C19 H16 F3 N3 O3
AKQXQLUNFKDZBN-UHFFFAOYSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
F
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
86W BindingDB:  7X2D Ki: min: 8.5, max: 21 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Structure summary