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- PDB-6cm4: Structure of the D2 Dopamine Receptor Bound to the Atypical Antip... -

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Basic information

Entry
Database: PDB / ID: 6cm4
TitleStructure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug Risperidone
ComponentsD(2) dopamine receptor, endolysin chimera
KeywordsMEMBRANE PROTEIN / GPCR / D2 / dopamine receptor / antipsychotic / risperidone
Function / homology
Function and homology information


negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / response to histamine / negative regulation of circadian sleep/wake cycle, sleep / regulation of synapse structural plasticity ...negative regulation of dopamine receptor signaling pathway / positive regulation of dopamine uptake involved in synaptic transmission / negative regulation of dephosphorylation / positive regulation of glial cell-derived neurotrophic factor production / acid secretion / dopamine neurotransmitter receptor activity, coupled via Gi/Go / nervous system process involved in regulation of systemic arterial blood pressure / response to histamine / negative regulation of circadian sleep/wake cycle, sleep / regulation of synapse structural plasticity / regulation of locomotion involved in locomotory behavior / neuron-neuron synaptic transmission / adenohypophysis development / negative regulation of dopamine secretion / positive regulation of renal sodium excretion / negative regulation of cellular response to hypoxia / hyaloid vascular plexus regression / adenylate cyclase-inhibiting dopamine receptor signaling pathway / response to inactivity / orbitofrontal cortex development / cerebral cortex GABAergic interneuron migration / regulation of potassium ion transport / Dopamine receptors / negative regulation of neuron migration / dopamine binding / branching morphogenesis of a nerve / regulation of dopamine uptake involved in synaptic transmission / positive regulation of growth hormone secretion / phospholipase C-activating dopamine receptor signaling pathway / peristalsis / heterotrimeric G-protein binding / drinking behavior / G protein-coupled receptor complex / grooming behavior / behavioral response to ethanol / auditory behavior / positive regulation of G protein-coupled receptor signaling pathway / striatum development / dopaminergic synapse / positive regulation of urine volume / positive regulation of multicellular organism growth / G protein-coupled receptor internalization / non-motile cilium / negative regulation of synaptic transmission, glutamatergic / heterocyclic compound binding / response to iron ion / adult walking behavior / arachidonate secretion / response to morphine / ciliary membrane / negative regulation of cytosolic calcium ion concentration / temperature homeostasis / regulation of synaptic transmission, GABAergic / positive regulation of neuroblast proliferation / pigmentation / positive regulation of cytokinesis / dopamine uptake involved in synaptic transmission / dopamine metabolic process / regulation of dopamine secretion / cellular response to ethanol / response to light stimulus / associative learning / positive regulation of receptor internalization / lateral plasma membrane / G-protein alpha-subunit binding / endocytic vesicle / neuroblast proliferation / negative regulation of protein secretion / long-term memory / sperm flagellum / potassium channel regulator activity / prepulse inhibition / postsynaptic modulation of chemical synaptic transmission / response to axon injury / viral release from host cell by cytolysis / regulation of sodium ion transport / behavioral response to cocaine / synapse assembly / negative regulation of blood pressure / cellular response to retinoic acid / release of sequestered calcium ion into cytosol / peptidoglycan catabolic process / axon terminus / ionotropic glutamate receptor binding / presynaptic modulation of chemical synaptic transmission / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / acrosomal vesicle / axonogenesis / regulation of heart rate / negative regulation of innate immune response / negative regulation of cell migration / response to amphetamine / epithelial cell proliferation / positive regulation of long-term synaptic potentiation / response to nicotine / excitatory postsynaptic potential / response to cocaine / locomotory behavior / phosphatidylinositol 3-kinase/protein kinase B signal transduction / circadian regulation of gene expression
Similarity search - Function
Dopamine D2 receptor / Dopamine receptor family / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx ...Dopamine D2 receptor / Dopamine receptor family / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8NU / OLEIC ACID / DI(HYDROXYETHYL)ETHER / Endolysin / D(2) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.867 Å
AuthorsWang, S. / Che, T. / Levit, A. / Shoichet, B.K. / Wacker, D. / Roth, B.L.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH61887 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)U19MH82441 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM59957 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016086 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nature / Year: 2018
Title: Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.
Authors: Wang, S. / Che, T. / Levit, A. / Shoichet, B.K. / Wacker, D. / Roth, B.L.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 14, 2018ID: 6C38
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: struct_ref_seq / Item: _struct_ref_seq.pdbx_auth_seq_align_beg
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D(2) dopamine receptor, endolysin chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4568
Polymers48,8791
Non-polymers1,5767
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint12 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.979, 72.523, 151.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D(2) dopamine receptor, endolysin chimera / Dopamine D2 receptor / Lysis protein / Lysozyme / Muramidase / Dopamine D2 receptor


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 / Plasmid: pFastBac1-HM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14416, UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-8NU / 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one


Mass: 410.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27FN4O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM Tris-HCl, pH 7.8, 230 mM lithium nitrate, 25% PEG400, 4% 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2017
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.867→30 Å / Num. obs: 12826 / % possible obs: 97.3 % / Redundancy: 5.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Net I/σ(I): 15.2
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1 / Num. unique obs: 889 / CC1/2: 0.535 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5WIU & 2RH1

5wiu

2rh1


Resolution: 2.867→29.549 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 622 4.85 %
Rwork0.2259 --
obs0.2271 12814 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.867→29.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 96 16 3236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033283
X-RAY DIFFRACTIONf_angle_d0.5164483
X-RAY DIFFRACTIONf_dihedral_angle_d10.8621928
X-RAY DIFFRACTIONf_chiral_restr0.037544
X-RAY DIFFRACTIONf_plane_restr0.003549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8674-3.15560.32141330.31662643X-RAY DIFFRACTION84
3.1556-3.61160.30341620.2733111X-RAY DIFFRACTION99
3.6116-4.54750.25111700.2093151X-RAY DIFFRACTION99
4.5475-29.55040.21881570.21033287X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.87040.78112.81812.96551.45074.73170.0593-0.10510.00930.1418-0.14640.13560.4299-0.3974-0.01370.3906-0.04090.02980.39480.03230.40977.65959.98831.8227
26.66971.65411.99416.88211.42056.4568-0.25510.1211-0.2547-0.3908-0.0566-0.46420.47110.23640.31470.69680.03630.08720.51980.10840.532.77-7.744636.3658
36.02440.35781.16985.38130.52096.7255-0.09480.33070.0832-0.40220.2772-0.05811.2902-0.0417-0.28470.63920.0087-0.09080.3770.0140.52769.8885-1.653-1.3224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 222 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1002 through 1161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 384 through 460 )

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