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- EMDB-55685: Cryo-EM structure of EA-RK-110-bound D3 dopamine receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-55685
TitleCryo-EM structure of EA-RK-110-bound D3 dopamine receptor
Map dataSharpened cryo-EM map of inactive D3 receptor, bound to EA-RK-110
Sample
  • Complex: GPCR-Go protein complex
    • Complex: inactive GPCR, fused to BRIL
      • Protein or peptide: D(3) dopamine receptor,Soluble cytochrome b562
    • Complex: BAG2 anti-BRIL Fab
      • Protein or peptide: BAG2 anti-BRIL Fab Heavy chain
      • Protein or peptide: BAG2 anti-BRIL Fab Light chain
  • Ligand: 3-[4-[2-[4-[3-cyano-5-(trifluoromethyl)phenyl]piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea
KeywordsGPCR / inverse-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 / G protein-coupled receptor internalization / 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 / social behavior / negative regulation of protein secretion / prepulse inhibition / negative regulation of blood pressure / behavioral response to cocaine / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of mitotic nuclear division / visual learning / learning / locomotory behavior / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transport chain / circadian regulation of gene expression / response to cocaine / intracellular calcium ion homeostasis / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G alpha (i) signalling events / learning or memory / electron transfer activity / periplasmic space / response to xenobiotic stimulus / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / synapse / plasma membrane
Similarity search - Function
Dopamine D3 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 / D(3) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYardeni EH / Kiss DJ / Shavit K / 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 D3 receptor bound to cariprazine reveals principles for partial agonists with designed pharmacology
Authors: Hadas Yardeni E / Kiss DJ / Sanchez J / Shavit K / Szepesi Kovacs D / Egyed A / Vogt CD / Gaitonde SA / Glenn J / Canals M / Bouvier M / Newman AH / Lane JR / Keseru GM / Shalev-Benami M
History
DepositionNov 12, 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_55685.png

Downloads & links

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Map

FileDownload / File: emd_55685.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of inactive D3 receptor, bound to EA-RK-110
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 336.92 Å		0.84 Å/pix.
x 400 pix.
= 336.92 Å		0.84 Å/pix.
x 400 pix.
= 336.92 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: 0.139
Minimum - Maximum-1.3117341 - 2.0989943
Average (Standard dev.)-0.000101362115 (±0.017145867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryo-EM map of inactive D3 receptor, bound to EA-RK-110

Fileemd_55685_additional_1.map
Annotationcryo-EM map of inactive D3 receptor, bound to EA-RK-110
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 inactive D3 receptor, bound to EA-RK-110

Fileemd_55685_half_map_1.map
AnnotationHalf map A of cryo-EM map of inactive D3 receptor, bound to EA-RK-110
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 inactive D3 receptor, bound to EA-RK-110

Fileemd_55685_half_map_2.map
AnnotationHalf map B of cryo-EM map of inactive D3 receptor, bound to EA-RK-110
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
    • Complex: inactive GPCR, fused to BRIL
      • Protein or peptide: D(3) dopamine receptor,Soluble cytochrome b562
    • Complex: BAG2 anti-BRIL Fab
      • Protein or peptide: BAG2 anti-BRIL Fab Heavy chain
      • Protein or peptide: BAG2 anti-BRIL Fab Light chain
  • Ligand: 3-[4-[2-[4-[3-cyano-5-(trifluoromethyl)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

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Supramolecule #2: inactive GPCR, fused to BRIL

SupramoleculeName: inactive GPCR, fused to BRIL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BAG2 anti-BRIL Fab

SupramoleculeName: BAG2 anti-BRIL Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: D(3) dopamine receptor,Soluble cytochrome b562

MacromoleculeName: D(3) dopamine receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.647766 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 YARIYVVARR QL ADLEDNW ETLNDNLKVI EKADNAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK LAN EGKVKE AQAAAEQLKT TRNAYIQKYL ERARSTLQKE VKATQMVAIV LGAFIVCWLP FFLTHVLNTH CQTCHVSPEL YSAT TWLGY VNSALNPVIY TTFNIEFRKA FLKILSC

UniProtKB: D(3) dopamine receptor, Soluble cytochrome b562, D(3) dopamine receptor

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Macromolecule #2: BAG2 anti-BRIL Fab Heavy chain

MacromoleculeName: BAG2 anti-BRIL Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.321084 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK S

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Macromolecule #3: BAG2 anti-BRIL Fab Light chain

MacromoleculeName: BAG2 anti-BRIL Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.483062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGE

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Macromolecule #4: 3-[4-[2-[4-[3-cyano-5-(trifluoromethyl)phenyl]piperazin-1-yl]ethy...

MacromoleculeName: 3-[4-[2-[4-[3-cyano-5-(trifluoromethyl)phenyl]piperazin-1-yl]ethyl]cyclohexyl]-1,1-dimethyl-urea
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1JUJ
Molecular weightTheoretical: 451.528 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: 13954333
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 273679
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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