[English] 日本語
Yorodumi
- EMDB-52624: Dopamine 1 receptor:GaS complex bound to 19B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52624
TitleDopamine 1 receptor:GaS complex bound to 19B
Map data
Sample
  • Complex: D1R complex with Gas and 19B
    • Protein or peptide: Beta-2 adrenergic receptor,D(1A) dopamine receptor
    • 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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
  • Ligand: 6-(4-imidazo[1,2-a]pyridin-8-yl-2-methyl-phenyl)-1,5-dimethyl-pyrimidine-2,4-dione
  • Ligand: water
KeywordsD1R / GS / AGONIST / PARKINSON / NEUROSCIENCE / D1R GS / HORMONE
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 / heterotrimeric G-protein binding / peristalsis ...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 / heterotrimeric G-protein binding / peristalsis / G protein-coupled receptor complex / modification of postsynaptic structure / positive regulation of neuron migration / habituation / grooming behavior / regulation of dopamine metabolic process / astrocyte development / dopamine transport / sensitization / striatum development / dentate gyrus development / positive regulation of potassium ion transport / conditioned taste aversion / maternal behavior / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / arrestin family protein binding / AMPA selective glutamate receptor signaling pathway / non-motile cilium / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction / long-term synaptic depression / positive regulation of cardiac muscle cell contraction / positive regulation of lipophagy / mating behavior / G protein-coupled dopamine receptor signaling pathway / adult walking behavior / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / : / ciliary membrane / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / endosome to lysosome transport / temperature homeostasis / dopamine metabolic process / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / transmission of nerve impulse / positive regulation of cAMP/PKA signal transduction / regulation of skeletal muscle contraction / adenylate cyclase binding / smooth muscle contraction / negative regulation of cardiac muscle cell apoptotic process / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / intracellular transport / G-protein alpha-subunit binding / potassium channel regulator activity / positive regulation of bone mineralization / bone resorption / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / D1 dopamine receptor binding / neuronal dense core vesicle / vascular endothelial cell response to laminar fluid shear stress / behavioral fear response / renal water homeostasis / activation of adenylate cyclase activity / neuronal action potential / Hedgehog 'off' state / intercellular bridge / regulation of sodium ion transport / cellular response to acidic pH / positive regulation of synaptic transmission, glutamatergic / adenylate cyclase-activating adrenergic receptor signaling pathway / behavioral response to cocaine / synapse assembly / cellular response to glucagon stimulus / positive regulation of cardiac muscle cell apoptotic process / intracellular glucose homeostasis / presynaptic modulation of chemical synaptic transmission / receptor-mediated endocytosis / brown fat cell differentiation / response to cold / adenylate cyclase activator activity / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / response to amphetamine / synaptic transmission, glutamatergic / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / clathrin-coated endocytic vesicle membrane
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor 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 ...Dopamine D1 receptor / Dopamine receptor family / Beta 2 adrenoceptor / Adrenoceptor 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / 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
Beta-2 adrenergic receptor / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsClairfeuille T / Rodriguez Sarmiento RM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Med Chem / Year: 2025
Title: Orally Bioavailable Dopamine D1/D5 Receptor-Biased Agonists to Study the Role of β-Arrestin in Treatment-Related Dyskinesia in Parkinson's Disease.
Authors: Rosa María Rodríguez Sarmiento / Stefan Berchtold / Nenad Manevski / Lothar Lindemann / Fabian Dey / Thomas Clairfeuille / Davide Amendola / Nicolas Vautrelle / Venceslas Duveau / Eoin C O Connor /
Abstract: Dopamine replacement therapies for Parkinson's disease often produce dyskinesias with long-term use. Published studies suggest that introducing β-arrestin signaling might be protective for ...Dopamine replacement therapies for Parkinson's disease often produce dyskinesias with long-term use. Published studies suggest that introducing β-arrestin signaling might be protective for dyskinesia. We advanced known noncatecholamine D1/D5 receptor G protein-biased agonists and found that removal of oxygen in the linker from published compounds limited β-arrestin recruitment, whereas introduction of nitrogen on the central -phenyl linker favored β-arrestin recruitment and provided orally bioavailable compounds. Cryogenic electron microscopy suggested key receptor-ligand interactions influencing the different bias behaviors. We discovered compound , a D1/D5 receptor agonist with β-arrestin recruitment and properties for use . We compared with tavapadon, which shows weak efficacy for β-arrestin signaling, in a rat model of Parkinson's disease with L-DOPA-induced dyskinesias. At particular doses, compound produced efficacy comparable to L-DOPA, but with fewer concomitant dyskinesias. This first study suggests that β-arrestin may have a positive influence on reducing dyskinesias following acute administration.
History
DepositionJan 27, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52624.png

Downloads & links

-
Map

FileDownload / File: emd_52624.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 288 pix.
= 268.992 Å		0.93 Å/pix.
x 288 pix.
= 268.992 Å		0.93 Å/pix.
x 288 pix.
= 268.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.934 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.88836247 - 1.2339894
Average (Standard dev.)-0.00010718278 (±0.017935837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 268.992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52624_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_52624_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52624_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52624_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : D1R complex with Gas and 19B

EntireName: D1R complex with Gas and 19B
Components
  • Complex: D1R complex with Gas and 19B
    • Protein or peptide: Beta-2 adrenergic receptor,D(1A) dopamine receptor
    • 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: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
  • Ligand: 6-(4-imidazo[1,2-a]pyridin-8-yl-2-methyl-phenyl)-1,5-dimethyl-pyrimidine-2,4-dione
  • Ligand: water

-
Supramolecule #1: D1R complex with Gas and 19B

SupramoleculeName: D1R complex with Gas and 19B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Beta-2 adrenergic receptor,D(1A) dopamine receptor

MacromoleculeName: Beta-2 adrenergic receptor,D(1A) dopamine receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.074711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS DYKDDDDKDM GQPGNGSAFL LAPNGSHAPD HDVTQERDEG GSENLYFQGG GSMRTLNTS AMDGTGLVVE RDFSVRILTA CFLSLLILST LLGNTLVCAA VIRFRHLRSK VTNFFVISLA VSDLLVAVLV M PWKAVAEI ...String:
MDSKGSSQKG SRLLLLLVVS NLLLCQGVVS DYKDDDDKDM GQPGNGSAFL LAPNGSHAPD HDVTQERDEG GSENLYFQGG GSMRTLNTS AMDGTGLVVE RDFSVRILTA CFLSLLILST LLGNTLVCAA VIRFRHLRSK VTNFFVISLA VSDLLVAVLV M PWKAVAEI AGFWPFGSFC NIWVAFDIMC STASILNLCV ISVDRYWAIS SPFRYERKMT PKAAFILISV AWTLSVLISF IP VQLSWHK AKPTSPSDGN ATSLAETIDN CDSSLSRTYA ISSSVISFYI PVAIMIVTYT RIYRIAQKQI RRIAALERAA VHA KNCQTT TGNGKPVECS QPESSFKMSF KRETKVLKTL SVIMGVFVCC WLPFFILNCI LPFCGSGETQ PFCIDSNTFD VFVW FGWAN SSLNPIIYAF NADFRKAFST LLGCYRLCPA TNNAIETVSI NNNGAAMFSS HHEPRGSISK ECNLVYLIPH AVGSS EDLK KEEAAGIARP LEKLSPALSV ILDYDTDVSL EKIQPITQNG QHPTHHHHHH HH

UniProtKB: Beta-2 adrenergic receptor, D(1A) dopamine receptor

-
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: 38.636199 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGHHHHHHHH SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT ...String:
MGHHHHHHHH SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLI IWDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR F LDDNQIVT SSGDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NA ICFFPNG NAFATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGH DNRVSC LGVTDDGMAV ATGSWDSFLK IWNG

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

-
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

-
Macromolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 4 / 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: 45.755547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ EALNLFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCS VDTENIRRVF NDCRDIIQRM HLRQYELL

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

-
Macromolecule #5: 6-(4-imidazo[1,2-a]pyridin-8-yl-2-methyl-phenyl)-1,5-dimethyl-pyr...

MacromoleculeName: 6-(4-imidazo[1,2-a]pyridin-8-yl-2-methyl-phenyl)-1,5-dimethyl-pyrimidine-2,4-dione
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1IZU
Molecular weightTheoretical: 346.383 Da

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA PLUNGER

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 936735
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more