+Open data
-Basic information
Entry | Database: PDB / ID: 6ps7 | ||||||
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Title | XFEL A2aR structure by ligand exchange from LUF5843 to ZM241385. | ||||||
Components | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / COMPLEX-LCP method / SBDD / drug design / XFEL / LCP-SFX / Ligand Exchange / Luf5843 / ZM241385 / A2aAR | ||||||
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 / 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 | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. ...Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Iucrj / Year: 2019 Title: Toward G protein-coupled receptor structure-based drug design using X-ray lasers. Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. ...Authors: Ishchenko, A. / Stauch, B. / Han, G.W. / Batyuk, A. / Shiriaeva, A. / Li, C. / Zatsepin, N. / Weierstall, U. / Liu, W. / Nango, E. / Nakane, T. / Tanaka, R. / Tono, K. / Joti, Y. / Iwata, S. / Moraes, I. / Gati, C. / Cherezov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ps7.cif.gz | 191.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ps7.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 6ps7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ps7_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 6ps7_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 6ps7_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 6ps7_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/6ps7 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/6ps7 | HTTPS FTP |
-Related structure data
Related structure data | 6przC 6ps0C 6ps1C 6ps2C 6ps3C 6ps4C 6ps5C 6ps6C 6ps8C 4eiyS 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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49386.484 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7 |
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-Non-polymers , 7 types, 133 molecules
#2: Chemical | ChemComp-ZMA / | ||||||||||
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#3: Chemical | ChemComp-OLC / ( #4: Chemical | #5: Chemical | ChemComp-OLB / ( | #6: Chemical | ChemComp-OLA / #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 50mM sodium thiocyanate, 100 mM sodium citrate pH 4.8, and 28% PEG 400, 2 mM of target ligand ZM241385 |
-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: 1.33 Å |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.33 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→33.5 Å / Num. obs: 45163 / % possible obs: 100 % / Redundancy: 118 % / CC1/2: 0.983 / R split: 0.136 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.85→1.9 Å / Num. unique obs: 3403 / CC1/2: 0.159 / R split: 2.17 |
Serial crystallography measurement | Focal spot size: 1.5 µm2 / Pulse duration: 30 fsec. / Pulse photon energy: 9.83 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Flow rate: 0.2 µL/min / Injector diameter: 50 µm |
Serial crystallography data reduction | Crystal hits: 68623 / Frames indexed: 39281 / Frames total: 241932 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4eiy Resolution: 1.85→33.494 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196.09 Å2 / Biso mean: 51.8642 Å2 / Biso min: 22.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→33.494 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 17.114 Å / Origin y: 198.4344 Å / Origin z: 18.2995 Å
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Refinement TLS group | Selection details: chain 'A' |