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Yorodumi- PDB-6s0l: Structure of the A2A adenosine receptor determined at SwissFEL us... -
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-Basic information
Entry | Database: PDB / ID: 6s0l | ||||||
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Title | Structure of the A2A adenosine receptor determined at SwissFEL using native-SAD at 4.57 keV from all available diffraction patterns | ||||||
Components | A2a adenosine receptor | ||||||
Keywords | SIGNALING PROTEIN / native-SAD / Serial femtosecond crystallography / SFX / SwissFEL / Jungfrau | ||||||
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 / response to amphetamine / presynaptic modulation of chemical synaptic transmission / astrocyte activation / 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-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / calmodulin binding / 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) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 2.65 Å | ||||||
Authors | Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. ...Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, J.C. | ||||||
Citation | Journal: Iucrj / Year: 2020 Title: Advances in long-wavelength native phasing at X-ray free-electron lasers. Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / ...Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Bacellar, C. / Bohinc, R. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s0l.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s0l.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s0l_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6s0l_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 6s0l_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 6s0l_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s0l ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s0l | HTTPS FTP |
-Related structure data
Related structure data | 6s0qC 6s19C 6s1dC 6s1eC 6s1gC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1650020 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.11577/1650021 / Data set type: diffraction image data |
Experimental dataset #3 | Data reference: 10.11577/1650022 / Data set type: diffraction image 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274*PLUS |
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-Non-polymers , 5 types, 15 molecules
#2: Chemical | ChemComp-ZMA / | ||||||
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#3: Chemical | ChemComp-OLA / #4: Chemical | #5: Chemical | #6: Chemical | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 297 K / Method: lipidic cubic phase Details: 0.1M sodium citrate pH 5.0, 0.05M sodium thiocyanate, 34% PEG400, 5mM ZM241385, 2% 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 297 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 2.713 Å |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Aug 12, 2018 / Frequency: 25 / Details: KB |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.713 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→35 Å / Num. obs: 29351 / % possible obs: 100 % / Redundancy: 858 % / Biso Wilson estimate: 117.58 Å2 / Net I/σ(I): 23.29 |
Reflection shell | Resolution: 2.65→35 Å / Num. unique obs: 29351 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→34.491 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.45 / 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: 2.65→34.491 Å
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Refine LS restraints |
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LS refinement shell |
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