[English] 日本語
Yorodumi- PDB-5vra: 2.35-Angstrom In situ Mylar structure of human A2A adenosine rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vra | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 2.35-Angstrom In situ Mylar structure of human A2A adenosine receptor at 100 K | ||||||||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562 chimera | ||||||||||||
Keywords | SIGNALING PROTEIN / In situ / GPCR / 7TM / LCP / fusion protein | ||||||||||||
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 / 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 / locomotory behavior / regulation of mitochondrial membrane potential / central nervous system development / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / electron transport chain / positive regulation of apoptotic signaling pathway / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||||||||
Authors | 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 | Germany, Canada, United States, 3items
| ||||||||||||
Citation | Journal: Nat Protoc / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vra.cif.gz | 251.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vra.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/5vra ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vra | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wjkC 5wktC 4eiyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7 |
---|
-Non-polymers , 7 types, 116 molecules
#2: Chemical | ChemComp-ZMA / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|