[English] 日本語
Yorodumi- PDB-3vga: Crystal structure of human adenosine A2A receptor with an alloste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vga | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 3.1 A resolution | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / 7 transmembrane receptor / SIGNAL TRANSDUCTION | ||||||
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 / calmodulin binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / dendrite / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / 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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. ...Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T. | ||||||
Citation | Journal: Nature / Year: 2012 Title: G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / ...Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vga.cif.gz | 296.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vga.ent.gz | 240.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/3vga ftp://data.pdbj.org/pub/pdb/validation_reports/vg/3vga | HTTPS FTP |
---|
-Related structure data
Related structure data | 3vg9C 1vgaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 36540.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1-316 / Mutation: N154Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: P29274 |
---|---|
#2: Antibody | Mass: 23527.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 24294.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#4: Chemical | ChemComp-ZMA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 400, 0.1M MES, 0.2M magnesium chloride, 0.5% octhyl thioglucoside , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2010 |
Radiation | Monochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→71.2 Å / Num. all: 18451 / Num. obs: 18451 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2700 / % possible all: 90.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VGA Resolution: 3.1→19.996 Å / SU ML: 0.83 / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: MLHL
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.174 Å2 / ksol: 0.304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→19.996 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|