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- PDB-7joz: Crystal structure of dopamine D1 receptor in complex with G prote... -

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Basic information

Entry
Database: PDB / ID: 7joz
TitleCrystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Endolysin,D(1A) dopamine receptor
  • Nanobody 35
KeywordsMEMBRANE PROTEIN / Dopamine receptor / D1 / non-catechol agonist / G protein
Function / homology
Function and homology information


dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / operant conditioning / cerebral cortex GABAergic interneuron migration / Dopamine receptors / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding ...dopamine neurotransmitter receptor activity, coupled via Gs / dopamine neurotransmitter receptor activity / operant conditioning / cerebral cortex GABAergic interneuron migration / Dopamine receptors / dopamine binding / regulation of dopamine uptake involved in synaptic transmission / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding / modification of postsynaptic structure / G protein-coupled receptor complex / regulation of dopamine metabolic process / positive regulation of neuron migration / grooming behavior / habituation / sensitization / dopamine transport / astrocyte development / dentate gyrus development / striatum development / conditioned taste aversion / positive regulation of potassium ion transport / maternal behavior / arrestin family protein binding / non-motile cilium / long-term synaptic depression / mating behavior / adult walking behavior / G protein-coupled dopamine receptor signaling pathway / ciliary membrane / temperature homeostasis / D-glucose import / dopamine metabolic process / transmission of nerve impulse / PKA activation in glucagon signalling / developmental growth / G-protein alpha-subunit binding / hair follicle placode formation / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / D1 dopamine receptor binding / intracellular transport / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / vascular endothelial cell response to laminar fluid shear stress / viral release from host cell by cytolysis / neuronal action potential / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / synapse assembly / behavioral response to cocaine / adenylate cyclase-activating adrenergic receptor signaling pathway / peptidoglycan catabolic process / cellular response to glucagon stimulus / presynaptic modulation of chemical synaptic transmission / regulation of insulin secretion / response to amphetamine / adenylate cyclase activator activity / positive regulation of release of sequestered calcium ion into cytosol / trans-Golgi network membrane / synaptic transmission, glutamatergic / negative regulation of inflammatory response to antigenic stimulus / G protein-coupled receptor activity / bone development / GABA-ergic synapse / visual learning / platelet aggregation / G-protein beta/gamma-subunit complex binding / vasodilation / cognition / memory / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / long-term synaptic potentiation / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / protein import into nucleus / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / cell wall macromolecule catabolic process / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / 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 / lysozyme / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events
Similarity search - Function
Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Dopamine D1 receptor / Dopamine receptor family / G-protein alpha subunit, group S / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / Serpentine type 7TM GPCR chemoreceptor Srsx / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / WD domain, G-beta repeat / 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 / Mainly Beta
Similarity search - Domain/homology
Chem-VFP / Endolysin / 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)
Lama glama (llama)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsSun, B. / Feng, D. / Chu, M.L. / Fish, I. / Kelm, S. / Lebon, F. / Lovera, S. / Valade, A. / Wood, M. / Ceska, T. ...Sun, B. / Feng, D. / Chu, M.L. / Fish, I. / Kelm, S. / Lebon, F. / Lovera, S. / Valade, A. / Wood, M. / Ceska, T. / Kobilka, T.S. / Sands, Z. / Kobilka, B.K.
CitationJournal: Nat Commun / Year: 2021
Title: Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist.
Authors: Sun, B. / Feng, D. / Chu, M.L. / Fish, I. / Lovera, S. / Sands, Z.A. / Kelm, S. / Valade, A. / Wood, M. / Ceska, T. / Kobilka, T.S. / Lebon, F. / Kobilka, B.K.
History
DepositionAug 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanobody 35
R: Endolysin,D(1A) dopamine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,5327
Polymers167,9315
Non-polymers6022
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-72 kcal/mol
Surface area61350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.194, 144.305, 147.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#1: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 44326.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63092
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38534.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59768

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Antibody / Protein , 2 types, 2 molecules NR

#4: Antibody Nanobody 35


Mass: 17352.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Protein Endolysin,D(1A) dopamine receptor / Lysis protein / Lysozyme / Muramidase / Dopamine D1 receptor


Mass: 59856.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, DRD1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9IEF7, UniProt: P21728, lysozyme

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-VFP / 6-{4-[(furo[3,2-c]pyridin-4-yl)oxy]-2-methylphenyl}-1,5-dimethylpyrimidine-2,4(1H,3H)-dione


Mass: 363.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1M MES pH 6.5, 0.1M Ammonium Dibasic Citrate, 18-25% (w/w) PEG400, 1mM TCEP, 10uM UCB1575401

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.79→49 Å / Num. obs: 20110 / % possible obs: 94.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 127.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.116 / Net I/σ(I): 4.7
Reflection shellResolution: 3.79→4.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.904 / Num. unique obs: 4783 / CC1/2: 0.468 / Rpim(I) all: 0.555 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SN6

3sn6


Resolution: 3.8→47 Å / SU ML: 0.5539 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2968 1057 5.3 %
Rwork0.2537 18897 -
obs0.2559 19954 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 139.93 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9116 0 43 0 9159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219333
X-RAY DIFFRACTIONf_angle_d0.524712769
X-RAY DIFFRACTIONf_chiral_restr0.0411514
X-RAY DIFFRACTIONf_plane_restr0.00311661
X-RAY DIFFRACTIONf_dihedral_angle_d13.38862967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.970.34791290.32442329X-RAY DIFFRACTION94
3.97-4.180.34081450.3032334X-RAY DIFFRACTION94.55
4.18-4.440.34281340.26622347X-RAY DIFFRACTION94.19
4.44-4.790.29081070.23632406X-RAY DIFFRACTION94.54
4.79-5.270.26951190.23622394X-RAY DIFFRACTION94.58
5.27-6.030.35311320.27412347X-RAY DIFFRACTION92.81
6.03-7.590.30211510.27842359X-RAY DIFFRACTION92.65
7.59-470.25211400.22022381X-RAY DIFFRACTION88.67
Refinement TLS params.Method: refined / Origin x: -2.32450069099 Å / Origin y: -38.0969843562 Å / Origin z: -40.5635125984 Å
111213212223313233
T0.665202171343 Å20.114221737637 Å20.027946723026 Å2-0.651552186511 Å20.107713312246 Å2--0.724362929799 Å2
L0.912552607484 °20.274074023268 °2-0.203773108359 °2-1.88053293054 °20.0571804696697 °2--0.710501460958 °2
S-0.124245629681 Å °-0.177174773653 Å °-0.295800033191 Å °0.11267166012 Å °-0.0746735832733 Å °-0.156304559488 Å °0.211308636198 Å °0.0746893203339 Å °0.183907265702 Å °
Refinement TLS groupSelection details: all

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