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- PDB-7dfp: Human dopamine D2 receptor in complex with spiperone -

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Basic information

Entry
Database: PDB / ID: 7dfp
TitleHuman dopamine D2 receptor in complex with spiperone
Components
  • D(2) dopamine receptor,Soluble cytochrome b562
  • FabH
  • FabL
KeywordsMEMBRANE PROTEIN / G-protein coupled receptor / Dopamine receptor / Spiperone / antipsychotic / Schizophrenia
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 / 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 / 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 / negative regulation of insulin secretion / electron transport chain
Similarity search - Function
Dopamine D2 receptor / Dopamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Dopamine D2 receptor / Dopamine receptor family / Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-SIP / Soluble cytochrome b562 / D(2) dopamine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsIm, D. / Shimamura, T. / Iwata, S.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the dopamine D 2 receptor in complex with the antipsychotic drug spiperone.
Authors: Im, D. / Inoue, A. / Fujiwara, T. / Nakane, T. / Yamanaka, Y. / Uemura, T. / Mori, C. / Shiimura, Y. / Kimura, K.T. / Asada, H. / Nomura, N. / Tanaka, T. / Yamashita, A. / Nango, E. / Tono, ...Authors: Im, D. / Inoue, A. / Fujiwara, T. / Nakane, T. / Yamanaka, Y. / Uemura, T. / Mori, C. / Shiimura, Y. / Kimura, K.T. / Asada, H. / Nomura, N. / Tanaka, T. / Yamashita, A. / Nango, E. / Tono, K. / Kadji, F.M.N. / Aoki, J. / Iwata, S. / Shimamura, T.
History
DepositionNov 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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_PubMed / _citation.title
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 6, 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: D(2) dopamine receptor,Soluble cytochrome b562
B: FabL
C: FabH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3144
Polymers87,9183
Non-polymers3951
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.900, 40.500, 165.900
Angle α, β, γ (deg.)90.000, 116.500, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein D(2) dopamine receptor,Soluble cytochrome b562 / Dopamine D2 receptor / Cytochrome b-562 / Cytochrome b-562 / Dopamine D2 receptor


Mass: 40590.652 Da / Num. of mol.: 1 / Mutation: S121K,L123W,M1007W,R1098I, H1102I, R1106G
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 35-220 from D(2) dopamine receptor, residues 23-62 and 88-128 from Soluble cytochrome b562, residues 364-443 from D(2) dopamine receptor.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: DRD2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14416, UniProt: P0ABE7
#2: Antibody FabL


Mass: 23884.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody FabH


Mass: 23443.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-SIP / 8-[4-(4-fluorophenyl)-4-oxidanylidene-butyl]-1-phenyl-1,3,8-triazaspiro[4.5]decan-4-one / Spiperone


Mass: 395.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26FN3O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 0.1M Lithium acetate dihydrate, 30% (V/V) polyethylene glycol 400, 5% (v/v) dimethyl sulfoxide, 0.01M Adenosine triphosphate, 1mM spiperone

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 3.1→43.12 Å / Num. obs: 18069 / % possible obs: 100 % / Redundancy: 99.8 % / Biso Wilson estimate: 73.4 Å2 / CC1/2: 0.97 / Net I/σ(I): 4.4
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 1757 / CC1/2: 0.58

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D3R (PDB ID: 3PBL)

3pbl


Resolution: 3.1→43.12 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 1087 6.02 %
Rwork0.1847 16961 -
obs0.1867 18048 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.39 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 29 0 5925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246054
X-RAY DIFFRACTIONf_angle_d0.56718265
X-RAY DIFFRACTIONf_chiral_restr0.0407979
X-RAY DIFFRACTIONf_plane_restr0.00451029
X-RAY DIFFRACTIONf_dihedral_angle_d13.23223600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.3191290.26552064X-RAY DIFFRACTION99.95
3.24-3.410.23531370.21842119X-RAY DIFFRACTION100
3.41-3.630.23281360.20522087X-RAY DIFFRACTION100
3.63-3.910.20211280.19432088X-RAY DIFFRACTION100
3.91-4.30.19671430.16622100X-RAY DIFFRACTION100
4.3-4.920.17821340.14932139X-RAY DIFFRACTION100
4.92-6.190.22031360.18372142X-RAY DIFFRACTION100
6.19-43.120.22581440.18112222X-RAY DIFFRACTION99.16
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)
12.40690217945-0.3242606309491.609388263141.501559564190.2256692138016.470016395960.10579986684-0.6415246462440.1973983577730.253518536034-0.296896576720.150305223170.0386191457299-0.9388303160570.1396687876441.34702765312-0.02235114272320.005401123532371.441803735-0.02100218443880.503297164136-95.1002929967-19.7507758185223.047760563
28.91387370081.90498274775.032631061337.876156406121.515396095765.53370108316-0.232854605573-0.6387299860660.919226618870.37781773910.05260610450280.744758250514-0.114581009306-1.14646539580.2333951845650.8743221990420.115283725676-0.07969360505771.23163787962-0.08977494474860.731735704539-71.51395722780.835746140792264.536792291
31.461442840840.4990516258472.796283889232.48340848693.031312480854.60508555470.130742997715-0.3510898362580.1583879610010.3791015557880.209185870088-0.05899121539710.1667530187390.926369174759-0.3325406750381.389074290390.0270899765594-0.1602979054991.62215379437-0.03593589234850.717590148516-83.9017381392-19.214962446233.740056143
46.1004021429-1.77736960182.184975114983.88336050991-4.560537344615.10214708398-0.309699074439-0.501417469116-0.4694704475260.01383254456830.929174110341.16514759934-0.228526763125-2.37681984943-0.666082624930.6516760140930.04099801928980.05605387947480.925071288966-0.08420621370680.682870978497-112.489458228-20.8512970271171.920704254
52.50817067705-0.000686008583482-0.1781633699951.549201288440.4816043232524.34362533975-0.139459209552-0.8452973933480.06533231920560.5418695574420.08256882400240.290453473506-0.300799424946-0.8399746069070.00491669865790.5162721080360.1664484006150.03998296735510.5884403592620.03931742462670.625882068228-106.558231104-18.5223520486172.908556334
65.96805229153-5.27361821217-3.471648187768.514410290314.953131399213.93533945697-0.232011193267-0.205717526026-0.1874715355070.09106459612410.1599673749850.4195635321260.09098296582750.1127956445080.004710955909850.295102399689-0.033031568638-0.06026329923340.2463941420650.09333124065450.543819789617-99.8031731407-31.3434268143145.567571899
79.46277249833-5.13375541585-4.972030509226.178238938435.273938280984.49187387838-0.126445291747-0.9790659175180.920636041853-0.4774150638250.383741340797-1.36412412096-0.9130048012910.723971354068-0.1698759738260.8509200640380.00510817831248-0.1686820337470.6417020595690.05390242831050.515220946761-83.177979137-21.1960230289178.206187247
86.941359423952.19092049812-2.048605616185.80512816466-1.882252960164.63994419330.0675255894304-1.517076252370.984920012711.01203443442-0.11929982774-0.168038129971-1.510864431560.3629868586630.0698559168990.8018813895850.0994450438366-0.1128264968950.694575043337-0.1562386341840.441318537979-88.9716307152-17.70770076186.995669633
95.769467475232.358152383531.55014074396.704870611842.88636480876.454543879340.0524951222193-1.01485540589-0.1565094182310.438289463874-0.2827608251550.370389331144-0.19627614638-1.052955352170.2347449983330.8574257282480.232856563179-0.03148184996460.9089019008450.08882486312290.338301001229-92.0256808361-26.7865102235188.942405004
102.679240898950.08878057316620.528089126858.913533809125.996103773976.71273660266-0.416643637602-1.01319757462-0.07532711631440.1211583532740.429687885009-0.01859890395190.2134527140860.5609224368570.06685573990370.796544160458-0.00759623431409-0.1983382130620.8114869849880.08275997546450.39531110621-84.154161359-26.8732773341183.868439703
111.8888092343-0.282850286341-2.028363734642.26997355881.294968520013.8258980096-0.370119796239-0.52887751139-0.06394945277570.6448368331350.180506341073-0.0650996761170.3787236374410.2395850773990.1934288870710.470089206020.0844885820145-0.1181383232820.3936375980670.07258775870780.547456289953-89.8694858668-21.7694134669174.561897882
123.48838990324-1.89047895491-3.023759487278.86051679497-1.101121648176.016647202180.5477100581930.587553794282-0.291711270025-1.42833166433-0.2239314829280.8198220140291.49011484476-0.999206795328-0.4467358467480.34690253925-0.0431897198912-0.1173781728030.3099485781570.01501935397030.596245884521-91.2681586078-23.8537083537140.960249042
133.51379278223-5.401127926475.753150313719.27061792738-8.849365653699.533004961810.3429907681580.02045384396260.3221740136090.172087395967-0.06310000902360.957773511199-0.0320189644972-0.206077502906-0.3629746288110.226763023705-0.0205228270020.009976002887460.287528762026-0.1347597049610.447325830224-83.2738147405-19.1515842225154.529997264
142.99802870236-0.5931634072151.742151064742.09363681692-2.93452401797.429380441750.0868019566434-0.06826910047360.0284389515059-0.1958820169240.0386226633090.150092194689-0.03400946600070.123521404037-0.1503479825810.2464224556760.048147828755-0.0311975695080.144970702506-0.06763929907250.54921113171-85.9468987859-20.1629301488147.374498498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 214 )
2X-RAY DIFFRACTION2(chain 'A' and (resid 215 through 216 )) or (chain 'A' and (resid 1003 through 1083))
3X-RAY DIFFRACTION3(chain 'A' and (resid 1084 through 1106 )) or (chain 'A' and (resid 364 through 442 ))
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 18 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 128 )
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 215 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'C' and (resid 18 through 40 )
9X-RAY DIFFRACTION9chain 'C' and (resid 41 through 73 )
10X-RAY DIFFRACTION10chain 'C' and (resid 74 through 91 )
11X-RAY DIFFRACTION11chain 'C' and (resid 92 through 131 )
12X-RAY DIFFRACTION12chain 'C' and (resid 132 through 152 )
13X-RAY DIFFRACTION13chain 'C' and (resid 153 through 164 )
14X-RAY DIFFRACTION14chain 'C' and (resid 165 through 220 )

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