8U02 | pdb_00008u02

CryoEM structure of D2 dopamine receptor in complex with GoA KE mutant and dopamine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8U02

This is version 1.2 of the entry. See complete history

Literature

A neurodevelopmental disorder mutation locks G proteins in the transitory pre-activated state.

Knight, K.M.Krumm, B.E.Kapolka, N.J.Ludlam, W.G.Cui, M.Mani, S.Prytkova, I.Obarow, E.G.Lefevre, T.J.Wei, W.Ma, N.Huang, X.P.Fay, J.F.Vaidehi, N.Smrcka, A.V.Slesinger, P.A.Logothetis, D.E.Martemyanov, K.A.Roth, B.L.Dohlman, H.G.

(2024) Nat Commun 15: 6643-6643

  • DOI: https://doi.org/10.1038/s41467-024-50964-z
  • Primary Citation Related Structures: 
    8TZQ, 8U02

  • PubMed Abstract: 

    Many neurotransmitter receptors activate G proteins through exchange of GDP for GTP. The intermediate nucleotide-free state has eluded characterization, due largely to its inherent instability. Here we characterize a G protein variant associated with a rare neurological disorder in humans. Gα o K46E has a charge reversal that clashes with the phosphate groups of GDP and GTP. As anticipated, the purified protein binds poorly to guanine nucleotides yet retains wild-type affinity for G protein βγ subunits. In cells with physiological concentrations of nucleotide, Gα o K46E forms a stable complex with receptors and Gβγ, impeding effector activation. Further, we demonstrate that the mutant can be easily purified in complex with dopamine-bound D2 receptors, and use cryo-electron microscopy to determine the structure, including both domains of Gα o , without nucleotide or stabilizing nanobodies. These findings reveal the molecular basis for the first committed step of G protein activation, establish a mechanistic basis for a neurological disorder, provide a simplified strategy to determine receptor-G protein structures, and a method to detect high affinity agonist binding in cells.


  • Organizational Affiliation
    • Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 138.22 kDa 
  • Atom Count: 7,774 
  • Modeled Residue Count: 1,013 
  • Deposited Residue Count: 1,226 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D(2) dopamine receptorA [auth R]443Homo sapiensMutation(s): 0 
Gene Names: DRD2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P14416 (Homo sapiens)
Explore P14416 
Go to UniProtKB:  P14416
PHAROS:  P14416
GTEx:  ENSG00000149295 
Entity Groups
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UniProt GroupP14416
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alpha354Homo sapiensMutation(s): 1 
Gene Names: GNAO1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens)
Explore P09471 
Go to UniProtKB:  P09471
PHAROS:  P09471
GTEx:  ENSG00000087258 
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UniProt GroupP09471
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth A]358Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth C]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LDP
(Subject of Investigation/LOI)

Query on LDP



Download:Ideal Coordinates CCD File
E [auth R]L-DOPAMINE
C8 H11 N O2
VYFYYTLLBUKUHU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LDP BindingDB:  8U02 Ki: min: 1.8, max: 1.50e+4 (nM) from 75 assay(s)
Kd: min: 6200, max: 2.67e+5 (nM) from 5 assay(s)
IC50: 0 (nM) from 1 assay(s)
EC50: min: 0.63, max: 3460 (nM) from 39 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesMH112205

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection