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- PDB-6luq: Haloperidol bound D2 dopamine receptor structure inspired discove... -

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Basic information

Entry
Database: PDB / ID: 6luq
TitleHaloperidol bound D2 dopamine receptor structure inspired discovery of subtype selective ligands
Componentschimera of D(2) dopamine receptor and Endolysin
KeywordsMEMBRANE PROTEIN / GPCR / Dopamine Receptor / Haloperidol / D2 Dopamine Receptor
Function / homology
Function and homology information


regulation of locomotion involved in locomotory behavior / negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of circadian sleep/wake cycle, sleep / acid secretion / positive regulation of glial cell-derived neurotrophic factor production / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / auditory behavior / regulation of synapse structural plasticity ...regulation of locomotion involved in locomotory behavior / negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of circadian sleep/wake cycle, sleep / acid secretion / positive regulation of glial cell-derived neurotrophic factor production / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / auditory behavior / regulation of synapse structural plasticity / response to histamine / positive regulation of renal sodium excretion / adenohypophysis development / neuron-neuron synaptic transmission / hyaloid vascular plexus regression / adenylate cyclase-inhibiting dopamine receptor signaling pathway / cerebral cortex GABAergic interneuron migration / negative regulation of neuron migration / response to inactivity / regulation of potassium ion transport / Dopamine receptors / orbitofrontal cortex development / dopamine binding / negative regulation of cellular response to hypoxia / regulation of dopamine uptake involved in synaptic transmission / branching morphogenesis of a nerve / negative regulation of voltage-gated calcium channel activity / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / heterotrimeric G-protein binding / dopaminergic synapse / drinking behavior / grooming behavior / peristalsis / phospholipase C-activating dopamine receptor signaling pathway / G protein-coupled receptor complex / behavioral response to ethanol / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of urine volume / striatum development / negative regulation of adenylate cyclase activity / negative regulation of synaptic transmission, glutamatergic / positive regulation of multicellular organism growth / response to morphine / non-motile cilium / G protein-coupled receptor internalization / adult walking behavior / response to iron ion / dopamine uptake involved in synaptic transmission / pigmentation / ciliary membrane / temperature homeostasis / regulation of synaptic transmission, GABAergic / arachidonic acid secretion / dopamine metabolic process / positive regulation of neuroblast proliferation / postsynaptic modulation of chemical synaptic transmission / regulation of dopamine secretion / heterocyclic compound binding / negative regulation of cytosolic calcium ion concentration / positive regulation of cytokinesis / behavioral response to cocaine / associative learning / positive regulation of receptor internalization / response to light stimulus / endocytic vesicle / neuroblast proliferation / negative regulation of protein secretion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / G-protein alpha-subunit binding / response to axon injury / potassium channel regulator activity / lateral plasma membrane / negative regulation of insulin secretion / long-term memory / sperm flagellum / prepulse inhibition / axon terminus / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / release of sequestered calcium ion into cytosol / viral release from host cell by cytolysis / synapse assembly / ionotropic glutamate receptor binding / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / negative regulation of blood pressure / regulation of heart rate / negative regulation of innate immune response / axonogenesis / peptidoglycan catabolic process / negative regulation of cell migration / response to cocaine / acrosomal vesicle / negative regulation of protein phosphorylation / locomotory behavior / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Dopamine D2 receptor / Dopamine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Dopamine D2 receptor / Dopamine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-GMJ / OLEIC ACID / Endolysin / D(2) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFan, L. / Tan, L. / Chen, Z. / Qi, J. / Nie, F. / Luo, Z. / Cheng, J. / Wang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB19000000 China
CitationJournal: Nat Commun / Year: 2020
Title: Haloperidol bound D2dopamine receptor structure inspired the discovery of subtype selective ligands.
Authors: Fan, L. / Tan, L. / Chen, Z. / Qi, J. / Nie, F. / Luo, Z. / Cheng, J. / Wang, S.
History
DepositionJan 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / entity_name_com / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chimera of D(2) dopamine receptor and Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3856
Polymers48,8791
Non-polymers1,5065
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-3 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.433, 72.820, 150.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein chimera of D(2) dopamine receptor and Endolysin / Dopamine D2 receptor / Lysis protein / Lysozyme / Muramidase


Mass: 48879.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: DRD2, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14416, UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-GMJ / 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one / Haloperidol / Haloperidol


Mass: 375.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClFNO2 / Details: Haloperidol / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antipsychotic*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris/HCl pH 7.5, 150 mM sodium malonate, 30% PEG400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 10160 / % possible obs: 93.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.3
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 1.13 / Num. unique obs: 1028

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CM4

6cm4


Resolution: 3.1→33.386 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.498 / SU ML: 0.373 / Cross valid method: FREE R-VALUE / ESU R Free: 0.437
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.229 468 4.747 %RANDOM
Rwork0.2152 ---
all0.216 ---
obs-9858 93.114 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.564 Å2
Baniso -1Baniso -2Baniso -3
1-1.871 Å20 Å20 Å2
2--1.617 Å20 Å2
3----3.488 Å2
Refinement stepCycle: LAST / Resolution: 3.1→33.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 106 10 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133337
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173142
X-RAY DIFFRACTIONr_ext_dist_refined_d00.011
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.6474541
X-RAY DIFFRACTIONr_angle_other_deg0.6011.5727176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27520.476147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64515470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621521
X-RAY DIFFRACTIONr_chiral_restr0.0470.2469
X-RAY DIFFRACTIONr_chiral_restr_other1.6220.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0520.023701
X-RAY DIFFRACTIONr_gen_planes_other0.0450.02746
X-RAY DIFFRACTIONr_nbd_refined0.2220.2924
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.23097
X-RAY DIFFRACTIONr_nbtor_refined0.180.21732
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1830.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.222
X-RAY DIFFRACTIONr_nbd_other0.2230.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.22
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.1-3.180.375330.3196900.3217750.6870.6993.29030.301
3.18-3.2660.353350.3126560.3147200.7110.75795.97220.288
3.266-3.360.303290.2686670.277380.8560.83794.30890.244
3.36-3.4620.285320.2685970.2686770.8670.86692.90990.236
3.462-3.5750.332320.246180.2446900.7770.87794.20290.205
3.575-3.6980.182200.2075930.2066600.9420.91392.87880.174
3.698-3.8360.229250.2075710.2086390.9180.9393.27070.18
3.836-3.9910.213380.195310.1926010.9270.94594.67550.168
3.991-4.1660.192290.1945430.1946080.9570.94194.07890.168
4.166-4.3650.194280.1854930.1865580.9530.94693.36920.174
4.365-4.5970.195310.1914870.1915540.950.95293.50180.176
4.597-4.870.198160.1714520.1725110.9580.95591.58510.158
4.87-5.1990.263260.1894330.1924970.920.95292.35410.175
5.199-5.6040.226180.2154060.2154620.9530.94691.77490.195
5.604-6.1220.276120.2543780.2554180.9380.94193.30140.226
6.122-6.8150.285180.243430.2423880.9520.94193.04120.216
6.815-7.8160.144100.193100.1883500.9710.96191.42860.197
7.816-9.4440.172120.162700.163040.9710.96892.76320.174
9.444-12.8510.141160.1982150.1942580.9680.95189.53490.222
12.851-33.3860.41180.3241360.3291650.7560.88587.27270.353

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