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- PDB-9bs9: Local refinement of DRD2 bound to LSD in complex with a mini-GoA ... -

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Basic information

Entry
Database: PDB / ID: 9bs9
TitleLocal refinement of DRD2 bound to LSD in complex with a mini-GoA and scFv16 obtained by cryo-electron microscopy (cryoEM)
ComponentsSoluble cytochrome b562,D(2) dopamine receptor
KeywordsMEMBRANE PROTEIN / GPCR / G-protein Coupled Receptor / DRD2 / serotonin / psychedelics
Function / homology
Function and homology information


negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / response to histamine / negative regulation of circadian sleep/wake cycle, sleep / regulation of synapse structural plasticity ...negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / response to histamine / negative regulation of circadian sleep/wake cycle, sleep / regulation of synapse structural plasticity / regulation of locomotion involved in locomotory behavior / neuron-neuron synaptic transmission / adenohypophysis development / negative regulation of dopamine secretion / positive regulation of renal sodium excretion / negative regulation of cellular response to hypoxia / hyaloid vascular plexus regression / adenylate cyclase-inhibiting dopamine receptor signaling pathway / orbitofrontal cortex development / cerebral cortex GABAergic interneuron migration / response to inactivity / regulation of potassium ion transport / Dopamine receptors / negative regulation of neuron migration / dopamine binding / branching morphogenesis of a nerve / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of growth hormone secretion / peristalsis / heterotrimeric G-protein binding / drinking behavior / G protein-coupled receptor complex / grooming behavior / behavioral response to ethanol / auditory behavior / positive regulation of G protein-coupled receptor signaling pathway / striatum development / dopaminergic synapse / positive regulation of urine volume / positive regulation of multicellular organism growth / G protein-coupled receptor internalization / non-motile cilium / heterocyclic compound binding / negative regulation of synaptic transmission, glutamatergic / response to iron ion / adult walking behavior / arachidonate secretion / ciliary membrane / response to morphine / negative regulation of cytosolic calcium ion concentration / temperature homeostasis / positive regulation of neuroblast proliferation / regulation of synaptic transmission, GABAergic / positive regulation of cytokinesis / pigmentation / dopamine metabolic process / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / response to light stimulus / cellular response to ethanol / associative learning / positive regulation of receptor internalization / lateral plasma membrane / neuroblast proliferation / G-protein alpha-subunit binding / endocytic vesicle / negative regulation of protein secretion / potassium channel regulator activity / long-term memory / sperm flagellum / prepulse inhibition / response to axon injury / postsynaptic modulation of chemical synaptic transmission / synapse assembly / negative regulation of blood pressure / regulation of sodium ion transport / behavioral response to cocaine / cellular response to retinoic acid / release of sequestered calcium ion into cytosol / axon terminus / ionotropic glutamate receptor binding / presynaptic modulation of chemical synaptic transmission / acrosomal vesicle / axonogenesis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of heart rate / negative regulation of innate immune response / negative regulation of cell migration / response to amphetamine / epithelial cell proliferation / positive regulation of long-term synaptic potentiation / response to nicotine / response to cocaine / excitatory postsynaptic potential / circadian regulation of gene expression / locomotory behavior / phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transport chain / negative regulation of insulin secretion
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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-7LD / Soluble cytochrome b562 / D(2) dopamine receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsKim, K. / Gumpper, R.H. / Fay, J.F. / Roth, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-20-2-0029 United States
CitationJournal: Neuron / Year: 2025
Title: The polypharmacology of psychedelics reveals multiple targets for potential therapeutics.
Authors: Manish K Jain / Ryan H Gumpper / Samuel T Slocum / Gavin P Schmitz / Jakob S Madsen / Tia A Tummino / Carl-Mikael Suomivuori / Xi-Ping Huang / Laura Shub / Jeffrey F DiBerto / Kuglae Kim / ...Authors: Manish K Jain / Ryan H Gumpper / Samuel T Slocum / Gavin P Schmitz / Jakob S Madsen / Tia A Tummino / Carl-Mikael Suomivuori / Xi-Ping Huang / Laura Shub / Jeffrey F DiBerto / Kuglae Kim / Chelsea DeLeon / Brain E Krumm / Jonathan F Fay / Michael Keiser / Alexander S Hauser / Ron O Dror / Brian Shoichet / David E Gloriam / David E Nichols / Bryan L Roth /
Abstract: The classical psychedelics (+)-lysergic acid diethylamide (LSD), psilocybin, and mescaline exert their psychedelic effects via activation of the 5-HT serotonin receptor (5-HTR). Recent clinical ...The classical psychedelics (+)-lysergic acid diethylamide (LSD), psilocybin, and mescaline exert their psychedelic effects via activation of the 5-HT serotonin receptor (5-HTR). Recent clinical studies have suggested that classical psychedelics may additionally have therapeutic potential for many neuropsychiatric conditions including depression, anxiety, migraine and cluster headaches, drug abuse, and post-traumatic stress disorder. In this study, we investigated the pharmacology of 41 classical psychedelics from the tryptamine, phenethylamine, and lysergamide chemical classes. We profiled these compounds against 318 human G-protein-coupled receptors (GPCRs) to elucidate their target profiles, and in the case of LSD, against more than 450 human kinases. We found that psychedelics have potent and efficacious actions at nearly every serotonin, dopamine, and adrenergic receptor. We quantified their activation for multiple transducers and found that psychedelics stimulate multiple 5-HTR transducers, each of which correlates with psychedelic drug-like actions in vivo. Our results suggest that multiple molecular targets likely contribute to the actions of psychedelics.
History
DepositionMay 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Soluble cytochrome b562,D(2) dopamine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5582
Polymers67,2351
Non-polymers3231
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 Soluble cytochrome b562,D(2) dopamine receptor / Cytochrome b-562 / Dopamine D2 receptor


Mass: 67234.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, DRD2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P14416
#2: Chemical ChemComp-7LD / (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide / Lysergic acid diethylamide


Mass: 323.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O / 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

ComponentName: DRD2 in complex mini-GoA / Type: COMPLEX / Entity ID: #1 / 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-PROPANE

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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: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2600 nm / Nominal defocus min: 170 nm
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2485527 / Symmetry type: POINT
RefinementHighest resolution: 2.28 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0062066
ELECTRON MICROSCOPYf_angle_d0.8982842
ELECTRON MICROSCOPYf_dihedral_angle_d4.617281
ELECTRON MICROSCOPYf_chiral_restr0.045369
ELECTRON MICROSCOPYf_plane_restr0.008336

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