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Yorodumi- PDB-3eml: The 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eml | ||||||
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Title | The 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bound to ZM241385. | ||||||
Components | Human Adenosine A2A receptor/T4 lysozyme chimera | ||||||
Keywords | MEMBRANE PROTEIN / RECEPTOR / adenosine / caffeine / GPCR / LCP / mesophase / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network | ||||||
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 / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / synaptic transmission, cholinergic / response to caffeine / intermediate filament / 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 / viral release from host cell by cytolysis / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / neuron projection morphogenesis / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / 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 wall macromolecule catabolic process / cell-cell signaling / lysozyme / presynaptic membrane / lysozyme activity / G alpha (s) signalling events / postsynaptic membrane / host cell cytoplasm / negative regulation of neuron apoptotic process / calmodulin binding / defense response to bacterium / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / dendrite / glutamatergic synapse / apoptotic process / lipid 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) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Jaakola, V.-P. / Griffith, M.T. / Hanson, M.A. / Cherezov, V. / Chien, E.Y.T. / Lane, J.R. / Ijzerman, A.P. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR) | ||||||
Citation | Journal: Science / Year: 2008 Title: The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist. Authors: Jaakola, V.P. / Griffith, M.T. / Hanson, M.A. / Cherezov, V. / Chien, E.Y. / Lane, J.R. / Ijzerman, A.P. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eml.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eml.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 3eml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3eml ftp://data.pdbj.org/pub/pdb/validation_reports/em/3eml | HTTPS FTP |
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-Related structure data
Related structure data | 2rh1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54739.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Plasmid: pBac5b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P00720 | ||||
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#2: Chemical | ChemComp-ZMA / | ||||
#3: Chemical | ChemComp-STE / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 13 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.79 % Description: THIS STRUCTURE IS A PART OF THE ROADMAP/PSI COMMUNITY OUTREACH PROGRAM, NOT A SPECIFIC PSI TARGET. |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: PEG400 30%v/v, LiSO4 185mM, NaCitrate 100mM, pH 6.5, Lipidic mesophase, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2008 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / 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→20 Å / Num. obs: 18465 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rsym value: 0.098 / Net I/σ(I): 7.35 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.398 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RH1 Resolution: 2.6→19.42 Å / SU ML: 0.43 / Isotropic thermal model: Isotropic / σ(F): 2 / 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: 78.49 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.42 Å
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LS refinement shell |
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