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Yorodumi- PDB-5k2d: 1.9A angstrom A2a adenosine receptor structure with MR phasing us... -
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-Basic information
Entry | Database: PDB / ID: 5k2d | ||||||
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Title | 1.9A angstrom A2a adenosine receptor structure with MR phasing using XFEL data | ||||||
Components | Adenosine receptor A2a/Soluble cytochrome b562 chimera | ||||||
Keywords | MEMBRANE PROTEIN / A2a adenosine receptor / Structural Genomics / PSI-Biology / GPCR Network / GPCR | ||||||
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 / 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 / locomotory behavior / regulation of mitochondrial membrane potential / central nervous system development / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / electron transport chain / positive regulation of apoptotic signaling pathway / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P. / Lee, M.-Y. / Stauch, B. / White, T.A. / Barty, A. ...Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P. / Lee, M.-Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / Liu, Z.-J. / Nelson, G. / James, D. / Li, C. / Zhao, Y. / Spence, J.C.H. / Liu, W. / Fromme, P. / Katritch, V. / Weierstall, U. / Stevens, R.C. / Cherezov, V. / GPCR Network (GPCR) | ||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. Authors: Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P.A. / Lee, M.Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / ...Authors: Batyuk, A. / Galli, L. / Ishchenko, A. / Han, G.W. / Gati, C. / Popov, P.A. / Lee, M.Y. / Stauch, B. / White, T.A. / Barty, A. / Aquila, A. / Hunter, M.S. / Liang, M. / Boutet, S. / Pu, M. / Liu, Z.J. / Nelson, G. / James, D. / Li, C. / Zhao, Y. / Spence, J.C. / Liu, W. / Fromme, P. / Katritch, V. / Weierstall, U. / Stevens, R.C. / Cherezov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k2d.cif.gz | 191.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k2d.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 5k2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/5k2d ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k2d | HTTPS FTP |
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-Related structure data
Related structure data | 5k2aC 5k2bC 5k2cC 4eiyS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49974.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens, Escherichia coli / Gene: ADORA2A, ADORA2,cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7 |
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-Non-polymers , 8 types, 120 molecules
#2: Chemical | ChemComp-ZMA / | ||||||||||
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#3: Chemical | ChemComp-NA / | ||||||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-OLC / ( #7: Chemical | ChemComp-OLA / #8: Chemical | ChemComp-PEG / | #9: 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: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 28 % (v/v) PEG 400, 40 mM sodium thiocyanate and 100 mM sodium citrate buffer pH 5.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.27 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 1, 2015 / Details: K-B mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→23.437 Å / Num. obs: 41882 / % possible obs: 100 % / Redundancy: 291 % / Biso Wilson estimate: 41 Å2 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 62 % / Mean I/σ(I) obs: 0.6 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.5 µm2 / Photons per pulse: 64000000000 Tphotons/pulse / Pulse duration: 35 fsec. / Pulse energy: 2.18 µJ / Pulse photon energy: 9.8 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Flow rate: 220 µL/min |
Serial crystallography data reduction | Crystal hits: 232283 / Frames indexed: 72735 / Frames total: 948961 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EIY Resolution: 1.9→23.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.82 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→23.44 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 |
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