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- EMDB-55650: Cryo-EM structure of ESG-2-36-bound D3 dopamine receptor with mini-Go -

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Basic information

Entry
Database: EMDB / ID: EMD-55650
TitleCryo-EM structure of ESG-2-36-bound D3 dopamine receptor with mini-Go
Map dataSharpened cryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36
Sample
  • Complex: GPCR-Go protein complex
    • Protein or peptide: D(3) dopamine receptor,Lgbit
    • 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: scFv16
  • Protein or peptide: Engineered miniGo,Guanine nucleotide-binding protein G(o) subunit alpha,Guanine nucleotide-binding protein G(o) subunit alpha
  • Ligand: 3-[4-[2-[4-(2-fluoranyl-3-methoxy-phenyl)piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea
KeywordsGPCR / agonist / MEMBRANE PROTEIN
Function / homology
Function and homology information


musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation ...musculoskeletal movement, spinal reflex action / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / response to histamine / regulation of potassium ion transport / Dopamine receptors / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / positive regulation of dopamine receptor signaling pathway / negative regulation of oligodendrocyte differentiation / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / G protein-coupled receptor internalization / G protein-coupled dopamine receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / arachidonate secretion / response to morphine / dopamine metabolic process / positive regulation of cytokinesis / negative regulation of cytosolic calcium ion concentration / regulation of dopamine secretion / parallel fiber to Purkinje cell synapse / social behavior / negative regulation of insulin secretion / negative regulation of protein secretion / prepulse inhibition / postsynaptic modulation of chemical synaptic transmission / negative regulation of blood pressure / behavioral response to cocaine / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of mitotic nuclear division / muscle contraction / visual learning / adenylate cyclase-inhibiting serotonin receptor signaling pathway / learning / G protein-coupled serotonin receptor binding / locomotory behavior / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / circadian regulation of gene expression / response to cocaine / intracellular calcium ion homeostasis / GABA-ergic synapse / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / 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 / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / G-protein beta-subunit binding / extracellular vesicle / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / GTPase binding / cell body / G protein activity / presynaptic membrane / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / learning or memory / postsynaptic membrane / Extra-nuclear estrogen signaling / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / lysosomal membrane
Similarity search - Function
Dopamine D3 receptor / Dopamine receptor family / G-protein alpha subunit, group I / 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 D3 receptor / Dopamine receptor family / G-protein alpha subunit, group I / 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
Guanine nucleotide-binding protein G(o) subunit alpha / D(3) 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsYardeni EH / Kiss DJ / Keseru GM / Shalev-Benami M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)949364European Union
CitationJournal: Sci Adv / Year: 2026
Title: The structure of the dopamine D receptor bound to cariprazine reveals principles for partial agonists with designed pharmacology.
Authors: Eliane Hadas Yardeni / Dóra Judit Kiss / Julie Sanchez / Keshet Shavit / Dénes Szepesi Kovács / Attila Egyed / Caleb D Vogt / Supriya A Gaitonde / Jacqueline Glenn / Meritxell Canals / ...Authors: Eliane Hadas Yardeni / Dóra Judit Kiss / Julie Sanchez / Keshet Shavit / Dénes Szepesi Kovács / Attila Egyed / Caleb D Vogt / Supriya A Gaitonde / Jacqueline Glenn / Meritxell Canals / Michel Bouvier / Amy Hauck Newman / J Robert Lane / György M Keserű / Moran Shalev-Benami /
Abstract: The third-generation antipsychotic cariprazine is a low-efficacy partial agonist of the dopamine D receptor (DR). Here, we report the cryo-electron microscopy structure of cariprazine bound to DR, ...The third-generation antipsychotic cariprazine is a low-efficacy partial agonist of the dopamine D receptor (DR). Here, we report the cryo-electron microscopy structure of cariprazine bound to DR, establishing a framework for understanding ligand recognition in this receptor. We further determine structures of DR in complex with a series of cariprazine derivatives spanning inverse agonists to high-efficacy partial agonists. Integration of structural data with pharmacological profiling and molecular dynamics simulations reveals how subtle chemical modifications translate into distinct functional outcomes. Determinants distinguishing agonism from inverse agonism are well defined, whereas differences among partial agonists arise from small positional shifts of the ligand within the orthosteric binding site. In contrast, the extended binding site primarily modulates ligand stability, affinity, and receptor selectivity. These findings establish a mechanistic link between bitopic ligand architecture and receptor activation, providing a "ligand-centric" view of DR signaling. Leveraging these principles, we designed and validated cariprazine derivatives with enhanced D/D selectivity and partial agonist activity. Together, this work provides a structural and pharmacological blueprint for the rational design of DR-targeting ligands with tailored efficacy and therapeutic profiles.
History
DepositionNov 11, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55650.png

Downloads & links

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Map

FileDownload / File: emd_55650.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 303.228 Å		0.84 Å/pix.
x 360 pix.
= 303.228 Å		0.84 Å/pix.
x 360 pix.
= 303.228 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8423 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.291
Minimum - Maximum-1.2925059 - 1.9742124
Average (Standard dev.)-0.00022258851 (±0.0317245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.228 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36

Fileemd_55650_additional_1.map
Annotationcryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of cryo-EM map of D3...

Fileemd_55650_half_map_1.map
AnnotationHalf map A of cryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of cryo-EM map of D3...

Fileemd_55650_half_map_2.map
AnnotationHalf map B of cryo-EM map of D3 receptor-G-protein complex, bound to ESG-2-36
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPCR-Go protein complex

EntireName: GPCR-Go protein complex
Components
  • Complex: GPCR-Go protein complex
    • Protein or peptide: D(3) dopamine receptor,Lgbit
    • 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: scFv16
  • Protein or peptide: Engineered miniGo,Guanine nucleotide-binding protein G(o) subunit alpha,Guanine nucleotide-binding protein G(o) subunit alpha
  • Ligand: 3-[4-[2-[4-(2-fluoranyl-3-methoxy-phenyl)piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea

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Supramolecule #1: GPCR-Go protein complex

SupramoleculeName: GPCR-Go protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: D(3) dopamine receptor,Lgbit

MacromoleculeName: D(3) dopamine receptor,Lgbit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.11873 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKGS GSENLYFQGG SMASLSQLSG HLNYTCGAEN STGASQARPH AYYALSYCAL ILAIVFGNGL VCMAVLKERA LQTTTNYLV VSLAVADLLV ATLVMPWVVY LEVTGGVWNF SRICCDVFVT LDVMMCTASI LNLCAISIDR YTAVVMPVHY Q HGTGQSSC ...String:
DYKDDDDKGS GSENLYFQGG SMASLSQLSG HLNYTCGAEN STGASQARPH AYYALSYCAL ILAIVFGNGL VCMAVLKERA LQTTTNYLV VSLAVADLLV ATLVMPWVVY LEVTGGVWNF SRICCDVFVT LDVMMCTASI LNLCAISIDR YTAVVMPVHY Q HGTGQSSC RRVALMITAV WVLAFAVSCP LLFGFNTTGD PTVCSISNPD FVIYSSVVSF YLPFGVTVLV YARIYVVLKQ RR RKRILTR QNSQCNSVRP GFPQQTLSPD PAHLELKRYY SICQDTALGG PGFQERGGEL KREEKTRNSL SPTIAPKLSL EVR KLSNGR LSTSLKLGPL QPRGVPLREK KATQMVAIVL GAFIVCWLPF FLTHVLNTHC QTCHVSPELY SATTWLGYVN SALN PVIYT TFNIEFRKAF LKILSCGSSG GGGSGGGGSS GVFTLEDFVG DWEQTAAYNL DQVLEQGGVS SLLQNLAVSV TPIQR IVRS GENALKIDIH VIIPYEGLSA DQMAQIEEVF KVVYPVDDHH FKVILPYGTL VIDGVTPNML NYFGRPYEGI AVFDGK KIT VTGTLWNGNK IIDERLITPD GSMLFRVTIN S

UniProtKB: D(3) dopamine receptor

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Macromolecule #2: Engineered miniGo,Guanine nucleotide-binding protein G(o) subunit...

MacromoleculeName: Engineered miniGo,Guanine nucleotide-binding protein G(o) subunit alpha,Guanine nucleotide-binding protein G(o) subunit alpha
type: protein_or_peptide / ID: 2 / 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: 25.248893 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTVSAEDKAA AERSKMIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT ...String:
MTVSAEDKAA AERSKMIEKN LKEDGISAAK DVKLLLLGAD NSGKSTIVKQ MKIIHGGSGG SGGTTGIVET HFTFKNLHFR LFDVGGQRS ERKKWIHCFE DVTAIIFCVD LSDYNRMHES LMLFDSICNN KFFIDTSIIL FLNKKDLFGE KIKKSPLTIC F PEYTGPNT YEDAAAYIQA QFESKNRSPN KEIYCHMTCA TDTNNAQVIF DAVTDIIIAN NLRGCGLY

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.729582 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WNGSSGGGGS GGGGSSGVSG WRLFKKIS

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

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Macromolecule #4: 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: 4 / 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 #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.340482 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KGSLEVLFQ

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Macromolecule #6: 3-[4-[2-[4-(2-fluoranyl-3-methoxy-phenyl)piperazin-1-yl]ethyl]cyc...

MacromoleculeName: 3-[4-[2-[4-(2-fluoranyl-3-methoxy-phenyl)piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1JUA
Molecular weightTheoretical: 406.537 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6543064
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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