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- PDB-5iub: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iub | ||||||
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Title | Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 12x at 2.1A resolution | ||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
![]() | MEMBRANE PROTEIN / G-protein-coupled receptor / integral membrane protein / chimera / thermostabilizing mutations | ||||||
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 / 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 / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / electron transport chain / positive regulation of 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Segala, E. / Guo, D. / Cheng, R.K.Y. / Bortolato, A. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Heitman, L.H. / Ijzerman, A.P. / Marshall, F.H. / Cooke, R.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength. Authors: Segala, E. / Guo, D. / Cheng, R.K. / Bortolato, A. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Heitman, L.H. / IJzerman, A.P. / Marshall, F.H. / Cooke, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.1 KB | Display | ![]() |
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PDB format | ![]() | 154.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.8 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iu4SC ![]() 5iu7C ![]() 5iu8C ![]() 5iuaC S: Starting model for refinement C: citing same article ( |
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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: 47996.746 Da / Num. of mol.: 1 Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, ...Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ADORA2A, ADORA2, cybC / Plasmid: pFAST-Bac / Cell line (production host): Tni PRO / Production host: ![]() |
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-Non-polymers , 7 types, 133 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/6DV.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/6DV.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-6DV / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-OLA / #6: Chemical | ChemComp-OLB / ( #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.36 % / Description: rectangular |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 0.1M MES pH 5.5, 0.2M K/Na tartrate, 27.5-40% PEG400, 0.5-1% (v/v) (+/-)-2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2014 / Details: (double) KB mirror pair |
Radiation | Monochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→33.62 Å / Num. obs: 27609 / % possible obs: 94.4 % / Redundancy: 5 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.5 / % possible all: 77.7 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5IU4 Resolution: 2.1→33.621 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.89 / 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: 2.1→33.621 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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