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- PDB-9t8d: Cryo-EM structure of EA-RK-110-bound D3 dopamine receptor -

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Basic information

Entry
Database: PDB / ID: 9t8d
TitleCryo-EM structure of EA-RK-110-bound D3 dopamine receptor
Components
  • BAG2 anti-BRIL Fab Heavy chain
  • BAG2 anti-BRIL Fab Light chain
  • D(3) dopamine receptor,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / inverse-agonist
Function / homology
Function and homology information


musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation ...musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation / G protein-coupled receptor internalization / negative regulation of synaptic transmission, glutamatergic / arachidonate secretion / response to morphine / dopamine metabolic process / positive regulation of cytokinesis / negative regulation of cytosolic calcium ion concentration / regulation of dopamine secretion / social behavior / negative regulation of protein secretion / prepulse inhibition / negative regulation of blood pressure / behavioral response to cocaine / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of mitotic nuclear division / visual learning / learning / locomotory behavior / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transport chain / circadian regulation of gene expression / response to cocaine / intracellular calcium ion homeostasis / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G alpha (i) signalling events / learning or memory / electron transfer activity / periplasmic space / response to xenobiotic stimulus / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / synapse / plasma membrane
Similarity search - Function
Dopamine D3 receptor / Dopamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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.
Similarity search - Domain/homology
: / Soluble cytochrome b562 / D(3) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYardeni, E.H. / Kiss, D.J. / Shavit, K. / Keseru, G.M. / Shalev-Benami, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)949364European Union
CitationJournal: Sci Adv / Year: 2026
Title: The structure of the dopamine D3 receptor bound to cariprazine reveals principles for partial agonists with designed pharmacology
Authors: Hadas Yardeni, E. / Kiss, D.J. / Sanchez, J. / Shavit, K. / Szepesi Kovacs, D. / Egyed, A. / Vogt, C.D. / Gaitonde, S.A. / Glenn, J. / Canals, M. / Bouvier, M. / Newman, A.H. / Lane, J.R. / ...Authors: Hadas Yardeni, E. / Kiss, D.J. / Sanchez, J. / Shavit, K. / Szepesi Kovacs, D. / Egyed, A. / Vogt, C.D. / Gaitonde, S.A. / Glenn, J. / Canals, M. / Bouvier, M. / Newman, A.H. / Lane, J.R. / Keseru, G.M. / Shalev-Benami, M.
History
DepositionNov 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 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

Downloads & links

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Assembly

Deposited unit
R: D(3) dopamine receptor,Soluble cytochrome b562
H: BAG2 anti-BRIL Fab Heavy chain
L: BAG2 anti-BRIL Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9034
Polymers95,4523
Non-polymers4521
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein D(3) dopamine receptor,Soluble cytochrome b562 / Dopamine D3 receptor / Cytochrome b-562


Mass: 47647.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: DRD3, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35462, UniProt: P0ABE7
#2: Antibody BAG2 anti-BRIL Fab Heavy chain


Mass: 24321.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody BAG2 anti-BRIL Fab Light chain


Mass: 23483.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-A1JUJ / 3-[4-[2-[4-[3-cyano-5-(trifluoromethyl)phenyl]piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea


Mass: 451.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32F3N5O / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeEntity IDParent-IDSource
1GPCR-Go protein complexCOMPLEX#1-#30MULTIPLE SOURCES
2inactive GPCR, fused to BRILCOMPLEX#11RECOMBINANT
3BAG2 anti-BRIL FabCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
32Escherichia coli (E. coli)562
43synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Escherichia coli (E. coli)562
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: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 38.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 13954333
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273679 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026094
ELECTRON MICROSCOPYf_angle_d0.5418338
ELECTRON MICROSCOPYf_dihedral_angle_d5.268867
ELECTRON MICROSCOPYf_chiral_restr0.063992
ELECTRON MICROSCOPYf_plane_restr0.0031043

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