+Open data
-Basic information
Entry | Database: PDB / ID: 7dfp | ||||||
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Title | Human dopamine D2 receptor in complex with spiperone | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / G-protein coupled receptor / Dopamine receptor / Spiperone / antipsychotic / Schizophrenia | ||||||
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 / auditory behavior / nervous system process involved in regulation of systemic arterial blood pressure / 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 / auditory behavior / nervous system process involved in regulation of systemic arterial blood pressure / regulation of synapse structural plasticity / response to histamine / positive regulation of renal sodium excretion / neuron-neuron synaptic transmission / adenohypophysis development / cerebral cortex GABAergic interneuron migration / regulation of potassium ion transport / hyaloid vascular plexus regression / negative regulation of neuron migration / Dopamine receptors / adenylate cyclase-inhibiting dopamine receptor signaling pathway / negative regulation of cellular response to hypoxia / orbitofrontal cortex development / response to inactivity / regulation of dopamine uptake involved in synaptic transmission / branching morphogenesis of a nerve / negative regulation of voltage-gated calcium channel activity / dopamine binding / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / heterotrimeric G-protein binding / behavioral response to ethanol / drinking behavior / peristalsis / G protein-coupled receptor complex / phospholipase C-activating dopamine receptor signaling pathway / dopaminergic synapse / grooming behavior / positive regulation of urine volume / positive regulation of G protein-coupled receptor signaling pathway / striatum development / negative regulation of adenylate cyclase activity / negative regulation of synaptic transmission, glutamatergic / positive regulation of multicellular organism growth / G protein-coupled receptor internalization / non-motile cilium / response to morphine / adult walking behavior / response to iron ion / ciliary membrane / regulation of synaptic transmission, GABAergic / arachidonate secretion / temperature homeostasis / pigmentation / dopamine uptake involved in synaptic transmission / postsynaptic modulation of chemical synaptic transmission / dopamine metabolic process / regulation of dopamine secretion / positive regulation of neuroblast proliferation / heterocyclic compound binding / negative regulation of cytosolic calcium ion concentration / positive regulation of cytokinesis / associative learning / positive regulation of receptor internalization / behavioral response to cocaine / endocytic vesicle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / G-protein alpha-subunit binding / neuroblast proliferation / response to light stimulus / sperm flagellum / response to axon injury / potassium channel regulator activity / GABA-ergic synapse / negative regulation of protein secretion / negative regulation of insulin secretion / long-term memory / prepulse inhibition / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / axon terminus / release of sequestered calcium ion into cytosol / epithelial cell proliferation / synapse assembly / response to amphetamine / presynaptic modulation of chemical synaptic transmission / negative regulation of blood pressure / ionotropic glutamate receptor binding / negative regulation of innate immune response / regulation of heart rate / phosphatidylinositol 3-kinase/protein kinase B signal transduction / axonogenesis / acrosomal vesicle / excitatory postsynaptic potential / negative regulation of protein phosphorylation / negative regulation of cell migration / response to cocaine / positive regulation of long-term synaptic potentiation / locomotory behavior / G protein-coupled receptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Im, D. / Shimamura, T. / Iwata, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dfp.cif.gz | 377.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dfp.ent.gz | 259.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dfp_validation.pdf.gz | 648.9 KB | Display | wwPDB validaton report |
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Full document | 7dfp_full_validation.pdf.gz | 652.7 KB | Display | |
Data in XML | 7dfp_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 7dfp_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfp ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfp | HTTPS FTP |
-Related structure data
Related structure data | 3pblS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1737551 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Antibody | Mass: 23884.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | 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 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.1→3.2 Å / Num. unique obs: 1757 / CC1/2: 0.58 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D3R (PDB ID: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→43.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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