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

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Basic information

Entry
Database: PDB / ID: 9lli
TitleCryo-EM structure of D1R in complex with de novo designed GEM targeting TM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
Components
  • D(1A) dopamine receptor
  • De novo designed GPCR exoframe modulator targeting TM1/2/4
  • De novo designed GPCR exoframe modulator targeting TM3/4/5
  • De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7
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 / peristalsis / heterotrimeric G-protein binding ...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 / peristalsis / heterotrimeric G-protein binding / modification of postsynaptic structure / G protein-coupled receptor complex / positive regulation of neuron migration / habituation / grooming behavior / regulation of dopamine metabolic process / dopamine transport / astrocyte development / dentate gyrus development / sensitization / striatum development / positive regulation of potassium ion transport / conditioned taste aversion / maternal behavior / arrestin family protein binding / non-motile cilium / G protein-coupled dopamine receptor signaling pathway / long-term synaptic depression / adult walking behavior / mating behavior / : / ciliary membrane / temperature homeostasis / dopamine metabolic process / transmission of nerve impulse / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / neuronal action potential / adenylate cyclase-activating adrenergic receptor signaling pathway / behavioral response to cocaine / synapse assembly / presynaptic modulation of chemical synaptic transmission / positive regulation of release of sequestered calcium ion into cytosol / response to amphetamine / synaptic transmission, glutamatergic / visual learning / G protein-coupled receptor activity / vasodilation / GABA-ergic synapse / memory / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein import into nucleus / long-term synaptic potentiation / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / presynaptic membrane / G alpha (s) signalling events / dendritic spine / postsynaptic membrane / positive regulation of MAPK cascade / cilium / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum membrane / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / 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
: / D(1A) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 modulators
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
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 negative allosteric GPCR exoframe modulator targeting TM5/6/7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9215
Polymers88,4874
Non-polymers4351
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 D(1A) dopamine receptor / Dopamine D1 receptor


Mass: 57222.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DRD1 / Production host: Homo sapiens (human) / References: UniProt: P21728
#2: Protein De novo designed GPCR exoframe modulator targeting TM1/2/4


Mass: 11438.839 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)
#3: 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)
#4: Protein De novo designed negative allosteric GPCR exoframe modulator targeting TM5/6/7


Mass: 10962.571 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)
#5: Chemical ChemComp-A1EKL / Flupentixol


Mass: 434.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25F3N2OS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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 with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
Type: COMPLEX / Entity ID: #1 / 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
IDNameCategory
1RELIONparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314295 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034574
ELECTRON MICROSCOPYf_angle_d0.5536211
ELECTRON MICROSCOPYf_dihedral_angle_d10.1711621
ELECTRON MICROSCOPYf_chiral_restr0.036758
ELECTRON MICROSCOPYf_plane_restr0.005719

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