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- PDB-9wg6: D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815 -

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Basic information

Entry
Database: PDB / ID: 9wg6
TitleD1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit
  • Nanobody35
KeywordsSTRUCTURAL PROTEIN / agonist / PAM / GPCR
Function / homology
Function and homology information


dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / G protein-coupled receptor complex ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / cerebral cortex GABAergic interneuron migration / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / dopamine binding / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / G protein-coupled receptor complex / modification of postsynaptic structure / adult walking behavior / positive regulation of potassium ion transport / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / non-motile cilium / arrestin family protein binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / AMPA selective glutamate receptor signaling pathway / G alpha (z) signalling events / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / norepinephrine binding / G protein-coupled dopamine receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenoceptors / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / positive regulation of lipophagy / positive regulation of cardiac muscle cell contraction / G alpha (i) signalling events / mating behavior / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / negative regulation of G protein-coupled receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / regulation of smooth muscle contraction / Ca2+ pathway / G alpha (z) signalling events / ciliary membrane / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G alpha (q) signalling events / G alpha (s) signalling events / adrenergic receptor signaling pathway / photoreceptor outer segment membrane / response to psychosocial stress / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (i) signalling events / dopamine metabolic process / endosome to lysosome transport / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / sensory perception of taste / positive regulation of glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / retina development in camera-type eye / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / transmission of nerve impulse / regulation of skeletal muscle contraction / negative regulation of cardiac muscle cell apoptotic process / adenylate cyclase binding / developmental growth / hair follicle placode formation / PKA activation in glucagon signalling / renal water homeostasis / cardiac muscle cell apoptotic process / intracellular transport / potassium channel regulator activity / G-protein alpha-subunit binding
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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 ...Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor family / G-protein alpha subunit, group S / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / 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
: / : / Chem-G4C / L-DOPAMINE / PALMITIC ACID / Beta-2 adrenergic receptor / D(1A) dopamine receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
Vicugna pacos (alpaca)
Oplophorus gracilirostris (arthropod)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsXu, Y. / Wang, K. / Zhuang, Y. / Xu, H.E.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130022 China
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)82495184 China
National Natural Science Foundation of China (NSFC)32401002 China
CitationJournal: To Be Published
Title: Molecular insights into the cooperative allosteric modulation of D1 dopamine receptor
Authors: Xu, Y. / Wang, K. / Zhuang, Y.
History
DepositionAug 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanobody35
R: Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,00311
Polymers161,0295
Non-polymers1,9746
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#1: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 29048.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P63092, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 40226.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54311
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7563.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212

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Antibody / Protein , 2 types, 2 molecules NR

#4: Antibody Nanobody35


Mass: 17352.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#5: Protein Beta-2 adrenergic receptor,D(1A) dopamine receptor,Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit / Beta-2 adrenoreceptor / Beta-2 adrenoceptor / Dopamine D1 receptor


Mass: 66836.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Engineered oplophorus-luciferin 2-monooxygenase catalytic subunit: PDB ID: 7SNY
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Oplophorus gracilirostris (arthropod)
Gene: ADRB2, ADRB2R, B2AR, DRD1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P07550, UniProt: P21728

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Non-polymers , 6 types, 7 molecules

#6: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#7: Chemical ChemComp-A1EWF / ~{N}-(3-aminocarbonyl-6-~{tert}-butyl-1-benzothiophen-2-yl)pyridine-4-carboxamide


Mass: 353.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-A1EV3 / 1-[(1~{S},3~{R},6~{R})-6-(1,3-benzodioxol-5-yl)-3-bicyclo[4.1.0]heptanyl]-4-[(2-bromanyl-5-chloranyl-phenyl)methyl]piperazine


Mass: 503.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28BrClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-G4C / 2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-3-oxidanyl-butyl)-3,4-dihydro-1H-isoquinolin-2-yl]ethanone


Mass: 450.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29Cl2NO3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: D1R-Gs-Nb35 complexes bound to Dopamine/LY3154207/BMSA1/UNC9815
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Rattus norvegicus (Norway rat)10116
41Bos taurus (domestic cattle)9913
51Vicugna pacos (alpaca)30538
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
31Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2cryoSPARC4.6particle selection
3PHENIX1.19.2_4158:model refinement
14cryoSPARC4.63D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209112 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038455
ELECTRON MICROSCOPYf_angle_d0.48411443
ELECTRON MICROSCOPYf_dihedral_angle_d5.1481168
ELECTRON MICROSCOPYf_chiral_restr0.0411281
ELECTRON MICROSCOPYf_plane_restr0.0041451

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