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Yorodumi- PDB-6iql: Crystal structure of dopamine receptor D4 bound to the subtype-se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iql | ||||||||||||
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Title | Crystal structure of dopamine receptor D4 bound to the subtype-selective ligand, L745870 | ||||||||||||
Components | D(4) dopamine receptor,Soluble cytochrome b562,D(4) dopamine receptor | ||||||||||||
Keywords | SIGNALING 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 | ||||||||||||
Biological species | Mus musculus (house mouse) Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Zhou, Y. / Cao, C. / Zhang, X.C. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iql.cif.gz | 274.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iql.ent.gz | 221.8 KB | Display | PDB format |
PDBx/mmJSON format | 6iql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iql_validation.pdf.gz | 836.9 KB | Display | wwPDB validaton report |
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Full document | 6iql_full_validation.pdf.gz | 847.5 KB | Display | |
Data in XML | 6iql_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 6iql_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iql ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iql | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 100 mM MES (pH 6.0), 50 mM ammonium citrate, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WIU, 1M6T Resolution: 3.5→20 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 317.41 Å2 / Biso mean: 182.4523 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→20 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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