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Yorodumi- PDB-5nm4: A2A Adenosine receptor room-temperature structure determined by s... -
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-Basic information
Entry | Database: PDB / ID: 5nm4 | ||||||
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Title | A2A Adenosine receptor room-temperature structure determined by serial femtosecond crystallography | ||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
Keywords | SIGNALING PROTEIN / room-temperature / serial crystallography | ||||||
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 / electron transport chain / 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 / periplasmic space / calmodulin binding / electron transfer activity / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / heme binding / 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) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 1.7 Å | ||||||
Authors | Weinert, T. / Cheng, R. / James, D. / Gashi, D. / Nogly, P. / Jaeger, K. / Hennig, M. / Standfuss, J. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / ...Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / Dore, A.S. / Geng, T. / Cooke, R.M. / Liang, M. / Prota, A.E. / Panneels, V. / Nogly, P. / Ermler, U. / Schertler, G. / Hennig, M. / Steinmetz, M.O. / Wang, M. / Standfuss, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nm4.cif.gz | 231.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nm4.ent.gz | 201.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nm4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5nm4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5nm4_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5nm4_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/5nm4 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/5nm4 | HTTPS FTP |
-Related structure data
Related structure data | 5njmC 5nlxC 5nm2C 5nm5C 5nqtC 5nquC 5o5wC 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7 |
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-Non-polymers , 5 types, 69 molecules
#2: Chemical | ChemComp-OLA / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ZMA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 291 K / Method: lipidic cubic phase / pH: 5 Details: 0.1M sodium citrate pH 5.0, 0.05M sodium thiocyanate, 28-34% PEG400, 5 mM ZM241385, 2% (v/v) 1,6-hexanediol |
-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: 1.3 Å |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20.2 Å / Num. obs: 56793 / % possible obs: 93.7 % / Redundancy: 23.3 % / CC1/2: 0.97 / R split: 0.1794 / Net I/σ(I): 2.93 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.44 / Num. unique obs: 3138 / CC1/2: 0.11 / R split: 3.1796 / % possible all: 53.59 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.587 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.08 / 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: 1.7→19.587 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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