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- PDB-5k2b: 2.5 angstrom A2a adenosine receptor structure with MR phasing usi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k2b | ||||||
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Title | 2.5 angstrom A2a adenosine receptor structure with MR phasing using XFEL data | ||||||
![]() | Adenosine receptor A2a/Soluble cytochrome b562 chimera | ||||||
![]() | MEMBRANE PROTEIN / A2a adenosine receptor / GPCR / Structural Genomics / PSI-Biology / GPCR Network | ||||||
Function / homology | ![]() 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 / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / locomotory behavior / positive regulation of long-term synaptic potentiation / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / electron transport chain / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k2aC ![]() 5k2cC ![]() 5k2dC ![]() 4eiyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() ![]() |
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-Non-polymers , 7 types, 86 molecules ![](data/chem/img/ZMA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZMA / | ||||||||
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#3: Chemical | ChemComp-NA / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-OLB / ( | #6: Chemical | ChemComp-OLC / ( #7: Chemical | ChemComp-OLA / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: 2.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→24 Å / Num. obs: 34140 / % possible obs: 100 % / Redundancy: 1022 % / Biso Wilson estimate: 41.5 Å2 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.6 / % possible all: 83.5 |
Serial crystallography measurement | Focal spot size: 1.5 µm2 / Photons per pulse: 170000000000 Tphotons/pulse / Pulse duration: 45 fsec. / Pulse energy: 2.77 µJ / 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: 1797503 / Frames indexed: 578620 / Frames total: 7324430 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EIY Resolution: 2.5→23.437 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.98 / 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: 2.5→23.437 Å
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Refine LS restraints |
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LS refinement shell |
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