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Yorodumi- PDB-5wiv: Structure of the sodium-bound human D4 Dopamine receptor in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wiv | |||||||||||||||
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Title | Structure of the sodium-bound human D4 Dopamine receptor in complex with Nemonapride | |||||||||||||||
Components | D(4) dopamine receptor, soluble cytochrome b562 chimera | |||||||||||||||
Keywords | SIGNALING PROTEIN/ANTAGONIST / GPCR / dopamine receptor / antagonist / sodium / SIGNALING PROTEIN-ANTAGONIST complex | |||||||||||||||
Function / homology | Function and homology information positive regulation of sodium:proton antiporter activity / positive regulation of dopamine uptake involved in synaptic transmission / dopamine neurotransmitter receptor activity, coupled via Gi/Go / epinephrine binding / response to histamine / dopamine neurotransmitter receptor activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase-inhibiting dopamine receptor signaling pathway / Dopamine receptors / negative regulation of voltage-gated calcium channel activity ...positive regulation of sodium:proton antiporter activity / positive regulation of dopamine uptake involved in synaptic transmission / dopamine neurotransmitter receptor activity, coupled via Gi/Go / epinephrine binding / response to histamine / dopamine neurotransmitter receptor activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase-inhibiting dopamine receptor signaling pathway / Dopamine receptors / negative regulation of voltage-gated calcium channel activity / dopamine binding / behavioral response to ethanol / regulation of dopamine metabolic process / fear response / serotonin binding / G protein-coupled serotonin receptor activity / inhibitory postsynaptic potential / positive regulation of kinase activity / regulation of postsynaptic neurotransmitter receptor internalization / norepinephrine binding / neurotransmitter receptor activity / arachidonate secretion / G protein-coupled dopamine receptor signaling pathway / dopamine metabolic process / behavioral response to cocaine / social behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral fear response / negative regulation of protein secretion / potassium channel regulator activity / response to amphetamine / adult locomotory behavior / electron transport chain / positive regulation of MAP kinase activity / regulation of circadian rhythm / SH3 domain binding / intracellular calcium ion homeostasis / rhythmic process / G alpha (i) signalling events / chemical synaptic transmission / postsynapse / periplasmic space / electron transfer activity / iron ion binding / centrosome / glutamatergic synapse / dendrite / heme binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å | |||||||||||||||
Authors | Wacker, D. / Wang, S. / Levit, A. / Che, T. / Betz, R.M. / McCorvy, J.D. / Venkatakrishnan, A.J. / Huang, X.-P. / Dror, R.O. / Shoichet, B.K. / Roth, B.L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Science / Year: 2017 Title: D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Authors: Wang, S. / Wacker, D. / Levit, A. / Che, T. / Betz, R.M. / McCorvy, J.D. / Venkatakrishnan, A.J. / Huang, X.P. / Dror, R.O. / Shoichet, B.K. / Roth, B.L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wiv.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wiv.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wiv_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5wiv_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5wiv_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 5wiv_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wiv ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wiv | HTTPS FTP |
-Related structure data
Related structure data | 5wiuSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45306.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: DRD4, cybC / Plasmid: pFastBac1-HM / Production host: Insecta (insects) / References: UniProt: P21917, UniProt: P0ABE7 |
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-Non-polymers , 6 types, 91 molecules
#2: Chemical | ChemComp-AQD / | ||||||||
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#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-OLA / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM Tris-HCl, pH 5.9-6.2, 100-140 mM ammonium phosphate dibasic, 180-200 mM sodium chloride, 34% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.143→30 Å / Num. obs: 24926 / % possible obs: 97.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.25 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.05 / Rrim(I) all: 0.122 / Χ2: 1.214 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5WIU Resolution: 2.143→29.687 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6 / Stereochemistry target values: ML
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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 max: 128.95 Å2 / Biso mean: 59.9002 Å2 / Biso min: 35.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.143→29.687 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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