+Open data
-Basic information
Entry | Database: PDB / ID: 3rfm | ||||||
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Title | Thermostabilised adenosine A2A receptor in complex with caffeine | ||||||
Components | Adenosine receptor A2a | ||||||
Keywords | SIGNALING PROTEIN / INVERSE AGONIST / 7TM / GPCR / G-PROTEIN / MEMBRANE 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 / NGF-independant TRKA activation ...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 / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / alpha-actinin binding / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / positive regulation of glutamate secretion / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / : / cellular defense response / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / phagocytosis / neuron projection morphogenesis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / astrocyte activation / excitatory postsynaptic potential / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / enzyme binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.598 Å | ||||||
Authors | Dore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. ...Dore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. / Tate, C.G. / Weir, M. / Marshall, F.H. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structure of the adenosine A(2A) receptor in complex with ZM241385 and the xanthines XAC and caffeine Authors: Dore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. / Tate, C.G. / Weir, M. / Marshall, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rfm.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rfm.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rfm_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 3rfm_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 3rfm_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3rfm_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/3rfm ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rfm | HTTPS FTP |
-Related structure data
Related structure data | 3pwhSC 3reyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36479.102 Da / Num. of mol.: 1 / Fragment: residues 1-317 Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274 |
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#2: Chemical | ChemComp-CFF / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.64 Å3/Da / Density % sol: 78.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 32-42% PEG1000, 0.25M MGCL2, 0.3% NG, 0.1%(W/V) 1-BUTANOL, 0.05% CYMAL-6, 0.1M TRIS-HCL,, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9777 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 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: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 3.59→50 Å / Num. obs: 8939 / % possible obs: 91.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.7 % / Biso Wilson estimate: 108.36 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.6→3.79 Å / Redundancy: 6.8 % / Num. unique all: 1328 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PWH Resolution: 3.598→19.971 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 42.96 / 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 / Bsol: 71.443 Å2 / ksol: 0.218 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 353.13 Å2 / Biso mean: 148.8877 Å2 / Biso min: 78.92 Å2
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Refinement step | Cycle: LAST / Resolution: 3.598→19.971 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 23.5394 Å / Origin y: -31.1724 Å / Origin z: -28.8621 Å
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Refinement TLS group | Selection details: chain A |