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- PDB-9u5f: cryo-EM structure of l-SPD binding to D2R -

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Basic information

Entry
Database: PDB / ID: 9u5f
Titlecryo-EM structure of l-SPD binding to D2R
Components
  • Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
  • heavy chain of Fab3089
  • light chain of Fab3089
KeywordsMEMBRANE PROTEIN / dopamine receptor / D1R / l-SPD / schizophrenia
Function / homology
Function and homology information


negative regulation of dephosphorylation / positive regulation of dopamine uptake involved in synaptic transmission / nervous system process involved in regulation of systemic arterial blood pressure / 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 ...negative regulation of dephosphorylation / positive regulation of dopamine uptake involved in synaptic transmission / nervous system process involved in regulation of systemic arterial blood pressure / 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 synapse structural plasticity / regulation of dopamine uptake involved in synaptic transmission / 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 / behavioral response to ethanol / dopaminergic synapse / non-motile cilium / G protein-coupled receptor internalization / 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 / Wnt signaling pathway / response to axon injury / associative learning / response to light stimulus / potassium channel regulator activity / positive regulation of receptor internalization / negative regulation of insulin secretion / negative regulation of protein secretion / regulation of dopamine secretion / lateral plasma membrane / G-protein alpha-subunit binding / endocytic vesicle / prepulse inhibition / postsynaptic modulation of chemical synaptic transmission / cellular response to retinoic acid / long-term memory / 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 / synapse assembly / visual learning / 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 / locomotory behavior / acrosomal vesicle / axon terminus / excitatory postsynaptic potential / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to cocaine / positive regulation of long-term synaptic potentiation / response to nicotine / circadian regulation of gene expression / autophagy / electron transport chain / GABA-ergic synapse / response to toxic substance / intracellular calcium ion homeostasis
Similarity search - Function
Dopamine D2 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
: / CHOLESTEROL / Soluble cytochrome b562 / Dopamine receptor D2
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, X.Y. / Liu, H. / Zhuang, Y.W. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM structure of l-SPD binding to D2R
Authors: Zhang, X.Y. / Liu, H. / Zhuang, Y.W.
History
DepositionMar 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 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: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
L: light chain of Fab3089
H: heavy chain of Fab3089
B: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,81710
Polymers145,6164
Non-polymers2,2016
Water00
1


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

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Components

#1: Protein Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562 / Dopamine D2 receptor / Cytochrome b-562


Mass: 49144.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: DRD2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14416, UniProt: P0ABE7
#2: Antibody light chain of Fab3089


Mass: 23884.314 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)
#3: Antibody heavy chain of Fab3089


Mass: 23443.117 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)
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1EN9 / (13~{a}~{S})-3,9-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[2,1-b]isoquinoline-2,10-diol / L-Stepholidine


Mass: 327.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21NO4
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: cryo-EM structure of l-SPD bound D1R-Gs complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176969 / Symmetry type: POINT

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