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Yorodumi- PDB-5mzp: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mzp | ||||||
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Title | Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with caffeine at 2.1A resolution | ||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
Keywords | MEMBRANE PROTEIN / G-PROTEIN-COUPLED RECEPTOR / INTEGRAL MEMBRANE PROTEIN / CHIMERA / THERMOSTABILIZING MUTATIONS | ||||||
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 / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / 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 / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / 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 / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / dendrite / neuronal cell body / lipid binding / glutamatergic synapse / apoptotic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cheng, K.Y.R. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity. Authors: Cheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mzp.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mzp.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/5mzp ftp://data.pdbj.org/pub/pdb/validation_reports/mz/5mzp | HTTPS FTP |
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-Related structure data
Related structure data | 5mzjC 5n2rC 5n2sC 5iu4S 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47996.746 Da / Num. of mol.: 1 Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, ...Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADORA2A, ADORA2, cybC / Plasmid: PFAST-BAC / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Tni PRO / References: UniProt: P29274, UniProt: P0ABE7 |
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-Non-polymers , 7 types, 209 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-CFF / | ||||||||
#4: Chemical | ChemComp-CLR / #5: Chemical | ChemComp-OLA / #6: Chemical | ChemComp-OLC / ( #7: Chemical | ChemComp-TAR / | #8: 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: 2.58 Å3/Da / Density % sol: 52.36 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016 / 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: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→89.94 Å / Num. obs: 29678 / % possible obs: 98.7 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2379 / CC1/2: 0.454 / Rpim(I) all: 0.532 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IU4 Resolution: 2.1→38.527 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.527 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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