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- PDB-5vra: 2.35-Angstrom In situ Mylar structure of human A2A adenosine rece... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vra | ||||||||||||
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Title | 2.35-Angstrom In situ Mylar structure of human A2A adenosine receptor at 100 K | ||||||||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562 chimera | ||||||||||||
![]() | SIGNALING PROTEIN / In situ / GPCR / 7TM / LCP / fusion protein | ||||||||||||
Function / homology | ![]() 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 / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / synaptic transmission, cholinergic / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / electron transport chain / positive regulation of apoptotic signaling pathway / 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 / periplasmic space / electron transfer activity / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Broecker, J. / Morizumi, T. / Ou, W.-L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.-Y. / Xu, S. / Makarov, O. ...Broecker, J. / Morizumi, T. / Ou, W.-L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.-Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / Ernst, O.P. | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Authors: Broecker, J. / Morizumi, T. / Ou, W.L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / Ernst, O.P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.7 KB | Display | ![]() |
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PDB format | ![]() | 202.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wjkC ![]() 5wktC ![]() 4eiyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 P29274 residues 2-208 and 219-316 linked by UNP P0ABE7 residues 23-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ADORA2A, ADORA2, cybC / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 116 molecules ![](data/chem/img/ZMA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZMA / | ||||||||
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#3: Chemical | ChemComp-NA / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-OLC / ( #6: Chemical | ChemComp-OLA / #7: Chemical | ChemComp-OLB / ( | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 25-28% PEG400, 0.04-0.06 M sodium thiocyanate, 2% 2,5-hexanediol, and 100 mM sodium citrate pH 5.0 PH range: 4.6-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→41.53 Å / Num. obs: 19560 / % possible obs: 91 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.53 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.154 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1384 / CC1/2: 0.56 / % possible all: 68 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4EIY Resolution: 2.35→41.419 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→41.419 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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