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- EMDB-41776: CryoEM structure of D2 dopamine receptor in complex with GoA KE m... -

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Entry
Database: EMDB / ID: EMD-41776
TitleCryoEM structure of D2 dopamine receptor in complex with GoA KE mutant and dopamine
Map data
Sample
  • Complex: Human DRD2 in complex with heterotrimeric G protein GoA (K46E) and dopamine
    • Protein or peptide: D(2) dopamine receptor
    • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: L-DOPAMINE
KeywordsGPCR / Dopamine / DRD2 / Dominant Negative / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of dopamine uptake involved in synaptic transmission / nervous system process involved in regulation of systemic arterial blood pressure / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / adenohypophysis development / regulation of defecation / negative regulation of dopamine receptor signaling pathway / negative regulation of circadian sleep/wake cycle, sleep / regulation of locomotion involved in locomotory behavior / acid secretion ...positive regulation of dopamine uptake involved in synaptic transmission / nervous system process involved in regulation of systemic arterial blood pressure / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / adenohypophysis development / regulation of defecation / negative regulation of dopamine receptor signaling pathway / negative regulation of circadian sleep/wake cycle, sleep / regulation of locomotion involved in locomotory behavior / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / neuron-neuron synaptic transmission / response to histamine / peristalsis / positive regulation of behavioral fear response / regulation of synaptic transmission, GABAergic / regulation of potassium ion transport / negative regulation of cellular response to hypoxia / response to inactivity / orbitofrontal cortex development / cerebral cortex GABAergic interneuron migration / dopamine neurotransmitter receptor activity / negative regulation of dopamine secretion / hyaloid vascular plexus regression / branching morphogenesis of a nerve / Dopamine receptors / drinking behavior / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / regulation of synapse structural plasticity / positive regulation of growth hormone secretion / phospholipase C-activating dopamine receptor signaling pathway / striatum development / heterotrimeric G-protein binding / beta-arrestin-dependent dopamine receptor signaling pathway / auditory behavior / adult walking behavior / positive regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor complex / dopaminergic synapse / mu-type opioid receptor binding / behavioral response to ethanol / corticotropin-releasing hormone receptor 1 binding / non-motile cilium / negative regulation of neurotransmitter secretion / G protein-coupled receptor internalization / G protein-coupled dopamine receptor signaling pathway / positive regulation of neuroblast proliferation / response to iron ion / negative regulation of synaptic transmission, glutamatergic / cellular response to ethanol / arachidonate secretion / ciliary membrane / response to morphine / dopamine metabolic process / positive regulation of cytokinesis / temperature homeostasis / regulation of sodium ion transport / negative regulation of cytosolic calcium ion concentration / response to axon injury / parallel fiber to Purkinje cell synapse / associative learning / response to light stimulus / potassium channel regulator activity / positive regulation of receptor internalization / regulation of dopamine secretion / negative regulation of insulin secretion / negative regulation of protein secretion / lateral plasma membrane / endocytic vesicle / G-protein alpha-subunit binding / prepulse inhibition / postsynaptic modulation of chemical synaptic transmission / long-term memory / cellular response to retinoic acid / sperm flagellum / regulation of long-term neuronal synaptic plasticity / negative regulation of blood pressure / release of sequestered calcium ion into cytosol / axonogenesis / behavioral response to cocaine / regulation of heart rate / response to amphetamine / Wnt signaling pathway / synapse assembly / visual learning / muscle contraction / presynaptic modulation of chemical synaptic transmission / negative regulation of innate immune response / adenylate cyclase-inhibiting dopamine receptor signaling pathway / negative regulation of cell migration / ionotropic glutamate receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / locomotory behavior / acrosomal vesicle / axon terminus / excitatory postsynaptic potential / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to cocaine
Similarity search - Function
Dopamine D2 receptor / Dopamine receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit ...Dopamine D2 receptor / Dopamine receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(o) subunit alpha / Dopamine receptor D2 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsKrumm BE / Kapolka NJ / Fay JF / Roth BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH112205 United States
CitationJournal: Nat Commun / Year: 2024
Title: A neurodevelopmental disorder mutation locks G proteins in the transitory pre-activated state.
Authors: Kevin M Knight / Brian E Krumm / Nicholas J Kapolka / W Grant Ludlam / Meng Cui / Sepehr Mani / Iya Prytkova / Elizabeth G Obarow / Tyler J Lefevre / Wenyuan Wei / Ning Ma / Xi-Ping Huang / ...Authors: Kevin M Knight / Brian E Krumm / Nicholas J Kapolka / W Grant Ludlam / Meng Cui / Sepehr Mani / Iya Prytkova / Elizabeth G Obarow / Tyler J Lefevre / Wenyuan Wei / Ning Ma / Xi-Ping Huang / Jonathan F Fay / Nagarajan Vaidehi / Alan V Smrcka / Paul A Slesinger / Diomedes E Logothetis / Kirill A Martemyanov / Bryan L Roth / Henrik G Dohlman /
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 ...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 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 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, 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.
History
DepositionAug 28, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41776.png

Downloads & links

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Map

FileDownload / File: emd_41776.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 356 pix.
= 311.144 Å		0.87 Å/pix.
x 356 pix.
= 311.144 Å		0.87 Å/pix.
x 356 pix.
= 311.144 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.874 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2542216 - 0.56153995
Average (Standard dev.)-0.00038653292 (±0.010698408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 311.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41776_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_41776_half_map_2.map
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Sample components

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Entire : Human DRD2 in complex with heterotrimeric G protein GoA (K46E) an...

EntireName: Human DRD2 in complex with heterotrimeric G protein GoA (K46E) and dopamine
Components
  • Complex: Human DRD2 in complex with heterotrimeric G protein GoA (K46E) and dopamine
    • Protein or peptide: D(2) dopamine receptor
    • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: L-DOPAMINE

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Supramolecule #1: Human DRD2 in complex with heterotrimeric G protein GoA (K46E) an...

SupramoleculeName: Human DRD2 in complex with heterotrimeric G protein GoA (K46E) and dopamine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: D(2) dopamine receptor

MacromoleculeName: D(2) dopamine receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.685355 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDPLNLSWYD DDLERQNWSR PFNGSDGKAD RPHYNYYATL LTLLIAVIVF GNVLVCMAVS REKALQTTTN YLIVSLAVAD LLVATLVMP WVVYLEVVGE WKFSRIHCDI FVTLDVMMCT ASILNLCAIS IDRYTAVAMP MLYNTRYSSK RRVTVMISIV W VLSFTISC ...String:
MDPLNLSWYD DDLERQNWSR PFNGSDGKAD RPHYNYYATL LTLLIAVIVF GNVLVCMAVS REKALQTTTN YLIVSLAVAD LLVATLVMP WVVYLEVVGE WKFSRIHCDI FVTLDVMMCT ASILNLCAIS IDRYTAVAMP MLYNTRYSSK RRVTVMISIV W VLSFTISC PLLFGLNNAD QNECIIANPA FVVYSSIVSF YVPFIVTLLV YIKIYIVLRR RRKRVNTKRS SRAFRAHLRA PL KGNCTHP EDMKLCTVIM KSNGSFPVNR RRVEAARRAQ ELEMEMLSST SPPERTRYSP IPPSHHQLTL PDPSHHGLHS TPD SPAKPE KNGHAKDHPK IAKIFEIQTM PNGKTRTSLK TMSRRKLSQQ KEKKATQMLA IVLGVFIICW LPFFITHILN IHCD CNIPP VLYSAFTWLG YVNSAVNPII YTTFNIEFRK AFLKILHC

UniProtKB: Dopamine receptor D2

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Macromolecule #2: Guanine nucleotide-binding protein G(o) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.100434 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGESTIV KQMKIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY ...String:
MGCTLSAEER AALERSKAIE KNLKEDGISA AKDVKLLLLG AGESGESTIV KQMKIIHEDG FSGEDVKQYK PVVYSNTIQS LAAIVRAMD TLGIEYGDKE RKADAKMVCD VVSRMEDTEP FSAELLSAMM RLWGDSGIQE CFNRSREYQL NDSAKYYLDS L DRIGAADY QPTEQDILRT RVKTTGIVET HFTFKNLHFR LFDVGGQRSE RKKWIHCFED VTAIIFCVAL SGYDQVLHED ET TNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC FPEYTGPNTY EDAAAYIQAQ FESKNRSPNK EIY CHMTCA TDTNNIQVVF DAVTDIIIAN NLRGCGLY

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #5: L-DOPAMINE

MacromoleculeName: L-DOPAMINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LDP
Molecular weightTheoretical: 153.178 Da
Chemical component information

ChemComp-LDP:
L-DOPAMINE / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8irs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153270
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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