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Yorodumi- PDB-5wf5: Agonist bound human A2a adenosine receptor with D52N mutation at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wf5 | ||||||
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Title | Agonist bound human A2a adenosine receptor with D52N mutation at 2.60 A resolution | ||||||
Components | Human A2a adenosine receptor T4L chimera | ||||||
Keywords | MEMBRANE PROTEIN / human A2a adenosine receptor / D52N / GPCR-T4L chimera / LCP / agonist / UK432097 / Activation microswitch / allosteric Na-site mutant / GPCR signaling | ||||||
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 / viral release from host cell by cytolysis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / astrocyte activation / peptidoglycan catabolic process / 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 wall macromolecule catabolic process / lysozyme / cell-cell signaling / lysozyme activity / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / host cell cytoplasm / calmodulin binding / defense response to bacterium / 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) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | White, K.L. / Eddy, M.T. / Gao, Z. / Han, G.W. / Hanson, M.A. / Lian, T. / Deary, A. / Patel, N. / Jacobson, K.A. / Katritch, V. / Stevens, R.C. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling. Authors: White, K.L. / Eddy, M.T. / Gao, Z.G. / Han, G.W. / Lian, T. / Deary, A. / Patel, N. / Jacobson, K.A. / Katritch, V. / 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 | 5wf5.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wf5.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wf5_validation.pdf.gz | 978.1 KB | Display | wwPDB validaton report |
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Full document | 5wf5_full_validation.pdf.gz | 972.5 KB | Display | |
Data in XML | 5wf5_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5wf5_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/5wf5 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/5wf5 | HTTPS FTP |
-Related structure data
Related structure data | 5wf6C 3emlS 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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 56555.074 Da / Num. of mol.: 1 / Mutation: R1012G C1054T C1097A I1137R Source method: isolated from a genetically manipulated source Details: D52N mutation Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: ADORA2A, ADORA2 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P29274, UniProt: P00720, lysozyme | ||
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#2: Chemical | ChemComp-UKA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.22 % |
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Crystal grow | Temperature: 296 K / Method: lipidic cubic phase Details: 100 mM sodium citrate pH 5, 24-27% (v/v) polyethylene glycol (PEG) 400, 30-80 mM MgCl 2 , 5% (v/v) Jeffamine M-600 pH 7 (Hampton) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 28, 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: 2.6→46.8 Å / Num. obs: 17786 / % possible obs: 92.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.503 / % possible all: 69.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3EML Resolution: 2.6→29.909 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.909 Å
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Refine LS restraints |
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LS refinement shell |
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