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- PDB-9llj: Cryo-EM structure of D1R-Gs in complex with de novo designed GEM ... -

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Basic information

Entry
Database: PDB / ID: 9llj
TitleCryo-EM structure of D1R-Gs in complex with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and agonist-positive allosteric GEM targeting TM5/6/7
Components
  • (De novo designed GPCR exoframe modulator targeting ...) x 2
  • (Guanine nucleotide-binding protein ...) x 2
  • D(1A) dopamine receptor,LgBiT
  • De novo designed agonist-positive allosteric GPCR exoframe modulator targeting TM5/6/7
  • Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
  • Nanoboy 35
KeywordsMEMBRANE PROTEIN / GPCR / GEM / GPCR exoframe modulator / D1R
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 / operant conditioning / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / peristalsis ...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 / operant conditioning / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / peristalsis / G protein-coupled receptor complex / modification of postsynaptic structure / positive regulation of neuron migration / habituation / grooming behavior / regulation of dopamine metabolic process / astrocyte development / striatum development / : / dentate gyrus development / positive regulation of potassium ion transport / sensitization / maternal behavior / conditioned taste aversion / arrestin family protein binding / non-motile cilium / G protein-coupled dopamine receptor signaling pathway / mating behavior / adult walking behavior / long-term synaptic depression / : / ciliary membrane / temperature homeostasis / dopamine metabolic process / 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 / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / intracellular transport / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / D1 dopamine receptor binding / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / behavioral fear response / Hedgehog 'off' state / activation of adenylate cyclase activity / neuronal action potential / cellular response to acidic pH / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / behavioral response to cocaine / synapse assembly / cellular response to glucagon stimulus / intracellular glucose homeostasis / presynaptic modulation of chemical synaptic transmission / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of insulin secretion involved in cellular response to glucose stimulus / adenylate cyclase activator activity / trans-Golgi network membrane / response to amphetamine / synaptic transmission, glutamatergic / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / bone development / visual learning / platelet aggregation / vasodilation / G protein-coupled receptor activity / GABA-ergic synapse / cognition / G-protein beta/gamma-subunit complex binding / memory / Olfactory Signaling Pathway / Activation of the phototransduction cascade / protein import into nucleus / positive regulation of insulin secretion / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sensory perception of smell / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor 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 ...Dopamine D1 receptor / Dopamine receptor 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
L-DOPAMINE / PALMITIC ACID / D(1A) dopamine receptor / 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 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsGuo, J. / Zhou, Y. / Cheng, S. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: GPCR exoframe modulator
Authors: Cheng, S. / Guo, J. / Zhou, Y. / Zhang, Y.
History
DepositionJan 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: D(1A) dopamine receptor,LgBiT
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanoboy 35
A: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
O: De novo designed GPCR exoframe modulator targeting TM1/2/4
P: De novo designed GPCR exoframe modulator targeting TM3/4/5
Q: De novo designed agonist-positive allosteric GPCR exoframe modulator targeting TM5/6/7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,35911
Polymers218,6938
Non-polymers6663
Water00
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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Protein , 3 types, 3 molecules RAQ

#1: Protein D(1A) dopamine receptor,LgBiT / Dopamine D1 receptor


Mass: 67994.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: DRD1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21728
#5: Protein Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 44284.074 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
#8: Protein De novo designed agonist-positive allosteric GPCR exoframe modulator targeting TM5/6/7


Mass: 9614.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules BC

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 41729.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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De novo designed GPCR exoframe modulator targeting ... , 2 types, 2 molecules OP

#6: Protein De novo designed GPCR exoframe modulator targeting TM1/2/4


Mass: 23206.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)
#7: Protein De novo designed GPCR exoframe modulator targeting TM3/4/5


Mass: 8862.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Antibody , 1 types, 1 molecules N

#4: Antibody Nanoboy 35


Mass: 15140.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 3 molecules

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


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Comment: medication*YM
#10: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2

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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: Complex of D1R-Gs with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and agonist-positive allosteric GEM targeting TM5/6/7
Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
8PHENIXmodel refinement
13cryoSPARC4.53D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216896 / Symmetry type: POINT
RefinementHighest resolution: 2.61 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210089
ELECTRON MICROSCOPYf_angle_d0.47313658
ELECTRON MICROSCOPYf_dihedral_angle_d5.2311369
ELECTRON MICROSCOPYf_chiral_restr0.041577
ELECTRON MICROSCOPYf_plane_restr0.0041689

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