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Yorodumi- PDB-5jtb: Crystal structure of the chimeric protein of A2aAR-BRIL with boun... -
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-Basic information
Entry | Database: PDB / ID: 5jtb | ||||||
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Title | Crystal structure of the chimeric protein of A2aAR-BRIL with bound iodide ions | ||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
Keywords | MEMBRANE PROTEIN / iodide | ||||||
Function / homology | Function and homology information positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / response to inorganic substance / cellular defense response / prepulse inhibition / phagocytosis / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / dendrite / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Melnikov, I. / Polovinkin, V. / Shevtsov, M. / Borshchevskiy, V. / Cherezov, V. / Popov, A. / Gordeliy, V. | ||||||
Citation | Journal: Sci Adv / Year: 2017 Title: Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G. ...Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G.A. / Gordeliy, V. / Popov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jtb.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jtb.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/5jtb ftp://data.pdbj.org/pub/pdb/validation_reports/jt/5jtb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49974.281 Da / Num. of mol.: 1 Fragment: UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316,UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316,UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7 |
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-Non-polymers , 8 types, 87 molecules
#2: Chemical | ChemComp-ZMA / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-IOD / #5: Chemical | #6: Chemical | ChemComp-OLA / #7: Chemical | ChemComp-OLC / ( #8: Chemical | ChemComp-OLB / ( | #9: 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: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.85 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.85 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 23712 / % possible obs: 0.997 % / Redundancy: 6.87 % / CC1/2: 0.997 / Rmerge(I) obs: 0.185 / Net I/σ(I): 8.83 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→89.9 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.869 / SU B: 28.975 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.95 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→89.9 Å
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