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Yorodumi- PDB-7pyr: Crystal structure of the adenosine A2A receptor (A2A-PSB1-bRIL) i... -
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-Basic information
Entry | Database: PDB / ID: 7pyr | ||||||||||||
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Title | Crystal structure of the adenosine A2A receptor (A2A-PSB1-bRIL) in complex with preladenant conjugate PSB-2115 | ||||||||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / A2A / G protein-coupled receptor / adenosine receptor / preladenant | ||||||||||||
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 / 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 | Homo sapiens (human) Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Claff, T. / Klapschinski, T.A. / Tiruttani Subhramanyam, U.K. / Vaassen, V.J. / Schlegel, J.G. / Vielmuth, C. / Voss, J.H. / Labahn, J. / Muller, C.E. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates. Authors: Claff, T. / Klapschinski, T.A. / Tiruttani Subhramanyam, U.K. / Vaassen, V.J. / Schlegel, J.G. / Vielmuth, C. / Voss, J.H. / Labahn, J. / Muller, C.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pyr.cif.gz | 230.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pyr.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 7pyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pyr_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
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Full document | 7pyr_full_validation.pdf.gz | 5.1 MB | Display | |
Data in XML | 7pyr_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 7pyr_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/7pyr ftp://data.pdbj.org/pub/pdb/validation_reports/py/7pyr | HTTPS FTP |
-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: 50016.379 Da / Num. of mol.: 1 / Mutation: S91K 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 , 6 types, 236 molecules
#2: Chemical | #3: Chemical | ChemComp-8IM / | #4: Chemical | ChemComp-OLA / #5: Chemical | ChemComp-OLC / ( #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 24% (v/v) PEG-400 (polyethylene glycol 400, average molecular weight 400), 10-30 mM sodium thiocyanate, 100 mM sodium citrate pH 5.2, and 2% (v/v) 2,5-hexanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 12, 2021 |
Radiation | Monochromator: Double crystal (Si-111 and Si-113 reflection) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.03 Å / Num. obs: 15875 / % possible obs: 97.92 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.88 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.26 |
Reflection shell | Resolution: 2.6→2.693 Å / Num. unique obs: 1545 / CC1/2: 0.585 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A2A model with PSB-2113 ligand Resolution: 2.6→45.03 Å / SU ML: 0.2894 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.9701 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 52.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.03 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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