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- EMDB-63871: cryo-EM structure of l-SPD binding to D2R -

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Basic information

Entry
Database: EMDB / ID: EMD-63871
Titlecryo-EM structure of l-SPD binding to D2R
Map data
Sample
  • Complex: cryo-EM structure of l-SPD bound D1R-Gs complex
    • Protein or peptide: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
    • Protein or peptide: light chain of Fab3089
    • Protein or peptide: heavy chain of Fab3089
  • Ligand: CHOLESTEROL
  • Ligand: (13~{a}~{S})-3,9-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[2,1-b]isoquinoline-2,10-diol
Keywordsdopamine receptor / D1R / l-SPD / schizophrenia / MEMBRANE PROTEIN
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
Soluble cytochrome b562 / Dopamine receptor D2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang XY / Liu H / Zhuang YW / Xu HE
Funding support China, 1 items
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 XY / Liu H / Zhuang YW
History
DepositionMar 21, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63871.png

Downloads & links

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Map

FileDownload / File: emd_63871.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 320 pix.
= 231.68 Å		0.72 Å/pix.
x 320 pix.
= 231.68 Å		0.72 Å/pix.
x 320 pix.
= 231.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.724 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.7723153 - 2.846379
Average (Standard dev.)0.0010421558 (±0.06317053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 231.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63871_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63871_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63871_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : cryo-EM structure of l-SPD bound D1R-Gs complex

EntireName: cryo-EM structure of l-SPD bound D1R-Gs complex
Components
  • Complex: cryo-EM structure of l-SPD bound D1R-Gs complex
    • Protein or peptide: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
    • Protein or peptide: light chain of Fab3089
    • Protein or peptide: heavy chain of Fab3089
  • Ligand: CHOLESTEROL
  • Ligand: (13~{a}~{S})-3,9-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[2,1-b]isoquinoline-2,10-diol

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Supramolecule #1: cryo-EM structure of l-SPD bound D1R-Gs complex

SupramoleculeName: cryo-EM structure of l-SPD bound D1R-Gs complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562

MacromoleculeName: Isoform 2 of D(2) dopamine receptor,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.144074 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDPLNLSWYD DDLERQNWSR PFNGSDGKAD RPHYNYYATL LTLLIAVIVF GNVLVCMAVS REKALQTTTN YLIVSLAVAD LLVATLVMP WVVYLEVVGE WKFSRIHCDI FVTLDVMMCT AKIWNLCAIS IDRYTAVAMP MLYNTRYSSK RRVTVMISIV W VLSFTISC ...String:
MDPLNLSWYD DDLERQNWSR PFNGSDGKAD RPHYNYYATL LTLLIAVIVF GNVLVCMAVS REKALQTTTN YLIVSLAVAD LLVATLVMP WVVYLEVVGE WKFSRIHCDI FVTLDVMMCT AKIWNLCAIS IDRYTAVAMP MLYNTRYSSK RRVTVMISIV W VLSFTISC PLLFGLNNAD QNECIIANPA FVVYSSIVSF YVPFIVTLLV YIKIYIVLRR RRARRQLADL EDNWETLNDN LK VIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLK TTRNAY IQKYLERARS TLSQQKEKKA TQMLAIVLGV FIICWLPFFI THILNIHCDC NIPPVLYSAF TWLGYVNSAV NPII YTTFN IEFRKAFLKI LHCHHHHHHH HHH

UniProtKB: Dopamine receptor D2, Soluble cytochrome b562, Dopamine receptor D2

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Macromolecule #2: light chain of Fab3089

MacromoleculeName: light chain of Fab3089 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.884314 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DIVMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGTVKLLLYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QYSKLPRTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGTVKLLLYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QYSKLPRTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNECN

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Macromolecule #3: heavy chain of Fab3089

MacromoleculeName: heavy chain of Fab3089 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.443117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EVQLQQSGAE LVKPGASVKI SCKASGYSFT GYNMNWVKQS RGKSLEWIGY INPFYGTTNY NQRFKGKATL TVDKSSSTAY IQLNSLTSE DSAVYYCARR YLTGTGAMDY WGQGTSVTVS SAKTTPPSVY PLAPGCGDTT GSSVTLGCLV KGYFPESVTV T WNSGSLSS ...String:
EVQLQQSGAE LVKPGASVKI SCKASGYSFT GYNMNWVKQS RGKSLEWIGY INPFYGTTNY NQRFKGKATL TVDKSSSTAY IQLNSLTSE DSAVYYCARR YLTGTGAMDY WGQGTSVTVS SAKTTPPSVY PLAPGCGDTT GSSVTLGCLV KGYFPESVTV T WNSGSLSS SVHTFPALLQ SGLYTMSSSV TVPSSTWPSQ TVTCSVAHPA SSTTVDKKLE PS

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: (13~{a}~{S})-3,9-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquin...

MacromoleculeName: (13~{a}~{S})-3,9-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[2,1-b]isoquinoline-2,10-diol
type: ligand / ID: 5 / Number of copies: 2 / Formula: A1EN9
Molecular weightTheoretical: 327.374 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176969
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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