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- EMDB-63870: cryo-EM structure of l-SPD bound D1R-Gs complex -

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Entry
Database: EMDB / ID: EMD-63870
Titlecryo-EM structure of l-SPD bound D1R-Gs complex
Map data
Sample
  • Complex: cryo-EM structure of l-SPD bound D1R-Gs complex
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Protein or peptide: Nanobody35
  • Protein or peptide: D(1A) dopamine receptor
  • 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


dopamine neurotransmitter receptor activity, coupled via Gs / cerebral cortex GABAergic interneuron migration / dopamine neurotransmitter receptor activity / Dopamine receptors / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / modification of postsynaptic structure ...dopamine neurotransmitter receptor activity, coupled via Gs / cerebral cortex GABAergic interneuron migration / dopamine neurotransmitter receptor activity / Dopamine receptors / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / heterotrimeric G-protein binding / 9+0 non-motile cilium / modification of postsynaptic structure / sensory perception of chemical stimulus / adult walking behavior / positive regulation of potassium ion transport / G protein-coupled receptor complex / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / arrestin family protein binding / non-motile cilium / G protein-coupled dopamine receptor signaling pathway / beta-2 adrenergic receptor binding / mating behavior / ciliary membrane / dopamine metabolic process / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / intracellular transport / regulation of skeletal muscle contraction / transmission of nerve impulse / hair follicle placode formation / developmental growth / PKA activation in glucagon signalling / renal water homeostasis / G-protein alpha-subunit binding / D1 dopamine receptor binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / vascular endothelial cell response to laminar fluid shear stress / Hedgehog 'off' state / activation of adenylate cyclase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / cellular response to acidic pH / positive regulation of synaptic transmission, glutamatergic / synapse assembly / ovarian follicle development / cellular response to glucagon stimulus / visual learning / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor binding / intracellular glucose homeostasis / positive regulation of release of sequestered calcium ion into cytosol / adenylate cyclase activator activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of insulin secretion / trans-Golgi network membrane / bone development / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / vasodilation / GABA-ergic synapse / platelet aggregation / cognition / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / sensory perception of smell / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / cilium / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit ...Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Serpentine type 7TM GPCR chemoreceptor Srsx / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G protein beta WD-40 repeat protein / G-protein, beta subunit / 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. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
D(1A) dopamine receptor / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 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_63870.png

Downloads & links

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Map

FileDownload / File: emd_63870.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.589979 - 4.020157
Average (Standard dev.)0.001466295 (±0.109053895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63870_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_63870_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63870_half_map_2.map
Projections & Slices
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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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Protein or peptide: Nanobody35
  • Protein or peptide: D(1A) dopamine receptor
  • 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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.790529 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GGSGGSMTED QRNEEKAQRE ANKMIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR IYHVNSGIFE TKFQVDKVNF HMFDVGAQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR ...String:
GGSGGSMTED QRNEEKAQRE ANKMIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR IYHVNSGIFE TKFQVDKVNF HMFDVGAQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR YTTPEDATPE PGEDPRVTRA KYFIRDEFLR ISTASGDGRH YCYPHFTCSV DTENARRIFN DCRDIIQRMH LR QYELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.915496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
MGSLLQSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Nanobody35

MacromoleculeName: Nanobody35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 15.271938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQVQLQESGG GLVQPGGSLR LSCAASGFTF SNYKMNWVRQ APGKGLEWVS DISQSGASIS YTGSVKGRFT ISRDNAKNTL YLQMNSLKP EDTAVYYCAR CPAPFTRDCF DVTSTTYAYR GQGTQVTVSS HHHHHHEPEA

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Macromolecule #5: D(1A) dopamine receptor

MacromoleculeName: D(1A) dopamine receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.339168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRTLNTSAMD GTGLVVERDF SVRILTACFL SLLILSTLLG NTLVCAAVIR FRHLRSKVTN FFVISLAVSD LLVAVLVMPW KAVAEIAGF WPFGSFCNIW VAFDIMCSTA SILNLCVISV DRYWAISSPF RYERKMTPKA AFILISVAWT LSVLISFIPV Q LSWHKAKP ...String:
MRTLNTSAMD GTGLVVERDF SVRILTACFL SLLILSTLLG NTLVCAAVIR FRHLRSKVTN FFVISLAVSD LLVAVLVMPW KAVAEIAGF WPFGSFCNIW VAFDIMCSTA SILNLCVISV DRYWAISSPF RYERKMTPKA AFILISVAWT LSVLISFIPV Q LSWHKAKP TSPSDGNATS LAETIDNCDS SLSRTYAISS SVISFYIPVA IMIVTYTRIY RIAQKQIRRI AALERAAVHA KN CQTTTGN GKPVECSQPE SSFKMSFKRE TKVLKTLSVI MGVFVCCWLP FFILNCILPF CGSGETQPFC IDSNTFDVFV WFG WANSSL NPIIYAFNAD FRKAFSTLLG CYRLCPATNN AIETVSINNN GAAMFSSHHE PRGSISKECN LVYLIPHAVG SSED LKKEE AAGIARPLEK LSPALSVILD YDTDVSLEKI QPITQNGQHP T

UniProtKB: D(1A) dopamine receptor

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Macromolecule #6: (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: 6 / Number of copies: 1 / 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: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 495756
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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