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- PDB-6iql: Crystal structure of dopamine receptor D4 bound to the subtype-se... -

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Basic information

Entry
Database: PDB / ID: 6iql
TitleCrystal structure of dopamine receptor D4 bound to the subtype-selective ligand, L745870
ComponentsD(4) dopamine receptor,Soluble cytochrome b562,D(4) dopamine receptor
KeywordsSIGNALING PROTEIN / GPCR / DRD4 / L745870 / ligand / dimerization
Function / homology
Function and homology information


Dopamine receptors / : / positive regulation of sodium:proton antiporter activity / dopamine neurotransmitter receptor activity, coupled via Gi/Go / : / response to histamine / : / epinephrine binding / dopamine neurotransmitter receptor activity / positive regulation of penile erection ...Dopamine receptors / : / positive regulation of sodium:proton antiporter activity / dopamine neurotransmitter receptor activity, coupled via Gi/Go / : / response to histamine / : / epinephrine binding / dopamine neurotransmitter receptor activity / positive regulation of penile erection / adenylate cyclase-inhibiting dopamine receptor signaling pathway / dopamine binding / negative regulation of voltage-gated calcium channel activity / G alpha (i) signalling events / regulation of dopamine metabolic process / negative regulation of vascular associated smooth muscle cell migration / regulation of neurotransmitter secretion / olfactory learning / short-term memory / vesicle membrane / fear response / synaptic transmission, dopaminergic / G protein-coupled serotonin receptor activity / inhibitory postsynaptic potential / positive regulation of kinase activity / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of synaptic transmission / norepinephrine binding / neurotransmitter receptor activity / G protein-coupled dopamine receptor signaling pathway / arachidonic acid secretion / regulation of synaptic vesicle exocytosis / regulation of postsynaptic membrane neurotransmitter receptor levels / plasma membrane => GO:0005886 / negative regulation of vascular associated smooth muscle cell proliferation / associative learning / positive regulation of excitatory postsynaptic potential / behavioral response to cocaine / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / GABA-ergic synapse / negative regulation of protein secretion / behavioral fear response / axon terminus / regulation of calcium-mediated signaling / response to amphetamine / adult locomotory behavior / electron transport chain / regulation of circadian rhythm / terminal bouton / SH3 domain binding / rhythmic process / cell cortex / chemical synaptic transmission / dendritic spine / periplasmic space / electron transfer activity / iron ion binding / axon / neuronal cell body / glutamatergic synapse / dendrite / heme binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Dopamine D4 receptor / Dopamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-L74 / Soluble cytochrome b562 / D(4) dopamine receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZhou, Y. / Cao, C. / Zhang, X.C.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910104 China
National Natural Science Foundation of China31470745 China
Chinese Academy of SciencesXDB08020301 China
CitationJournal: Elife / Year: 2019
Title: Crystal structure of dopamine receptor D4 bound to the subtype selective ligand, L745870.
Authors: Zhou, Y. / Cao, C. / He, L. / Wang, X. / Zhang, X.C.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D(4) dopamine receptor,Soluble cytochrome b562,D(4) dopamine receptor
B: D(4) dopamine receptor,Soluble cytochrome b562,D(4) dopamine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7854
Polymers87,1312
Non-polymers6542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-16 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 142.000, 146.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein D(4) dopamine receptor,Soluble cytochrome b562,D(4) dopamine receptor / D(2C) dopamine receptor / Dopamine D4 receptor / Cytochrome b-562


Mass: 43565.680 Da / Num. of mol.: 2 / Mutation: F121W,C181R,P201I,M1007W,H1106L,P317A,G307A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of dopamine receptor D4 (residues 23-218), cytochrome b562 (residues 23-127), Linker and dopamine receptor D4 (residues 304-387).
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Escherichia coli (E. coli)
Gene: Drd4, cybC / Plasmid: pFastBac1 / Cell line (production host): High5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51436, UniProt: P0ABE7
#2: Chemical ChemComp-L74 / 3-{[4-(4-chlorophenyl)piperazin-1-yl]methyl}-1H-pyrrolo[2,3-b]pyridine


Mass: 326.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19ClN4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antipsychotic, antagonist*YM
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM MES (pH 6.0), 50 mM ammonium citrate, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 13628 / % possible obs: 97 % / Redundancy: 5.427 % / Biso Wilson estimate: 161.8 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.253 / Χ2: 0.837 / Net I/σ(I): 3.19
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3.4-3.650.936710.55195
3.6-3.85.871.7213970.84198.9
3.8-45.832.8125000.887198.7
4-4.55.653.8716170.98198.5
4.5-55.34.8733160.955197.7
5-84.127.565420.981198.4
8-105.277.724240.987197.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WIU, 1M6T

5wiu

1m6t


Resolution: 3.5→20 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.59
RfactorNum. reflection% reflection
Rfree0.336 636 4.99 %
Rwork0.306 --
obs0.307 12748 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 317.41 Å2 / Biso mean: 182.4523 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 46 0 5013
Biso mean--209.13 --
Num. residues----681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5003-3.770.43011180.3943233398
3.77-4.14840.40871250.37482403100
4.1484-4.74640.38811310.33362408100
4.7464-5.97130.36291250.3754241099
5.9713-200.29621370.254255899

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