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Yorodumi- PDB-7m8w: XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m8w | ||||||
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Title | XFEL crystal structure of the prostaglandin D2 receptor CRTH2 in complex with 15R-methyl-PGD2 | ||||||
Components | Prostaglandin D2 receptor 2, Endolysin chimera | ||||||
Keywords | MEMBRANE PROTEIN / prostaglandin D2 receptor / CRTH2 / 15R-methyl-PGD2 / G protein-coupled receptor / GPCR / Endolysin fusion / LCP | ||||||
Function / homology | Function and homology information prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway ...prostaglandin J receptor activity / prostaglandin D receptor activity / prostaglandin F receptor activity / Prostanoid ligand receptors / negative regulation of male germ cell proliferation / positive regulation of G protein-coupled receptor signaling pathway / neuropeptide binding / neuropeptide signaling pathway / viral release from host cell by cytolysis / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / peptidoglycan catabolic process / G protein-coupled receptor activity / calcium-mediated signaling / chemotaxis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / defense response to bacterium / neuron projection / immune response / G protein-coupled receptor signaling pathway / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Shiriaeva, A. / Han, G.W. / Cherezov, V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2. Authors: Liu, H. / Deepak, R.N.V.K. / Shiriaeva, A. / Gati, C. / Batyuk, A. / Hu, H. / Weierstall, U. / Liu, W. / Wang, L. / Cherezov, V. / Fan, H. / Zhang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m8w.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m8w.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 7m8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m8w_validation.pdf.gz | 815.8 KB | Display | wwPDB validaton report |
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Full document | 7m8w_full_validation.pdf.gz | 820.2 KB | Display | |
Data in XML | 7m8w_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7m8w_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/7m8w ftp://data.pdbj.org/pub/pdb/validation_reports/m8/7m8w | HTTPS FTP |
-Related structure data
Related structure data | 6d27S S: Starting model for refinement |
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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: 52228.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: PTGDR2, CRTH2, DL1R, GPR44, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Y4, UniProt: D9IEF7 |
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-Non-polymers , 5 types, 20 molecules
#2: Chemical | ChemComp-YSS / | ||
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#3: Chemical | ChemComp-NA / | ||
#4: Chemical | ChemComp-FLC / | ||
#5: Chemical | ChemComp-SO4 / #6: 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: 20358 |
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-Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.22 % |
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Crystal grow | Temperature: 283 K / Method: lipidic cubic phase / pH: 6 Details: sodium chloride, lithium sulphate, sodium citrate tribasic dihydrate, PEG 300, propylene glycol P400, PGD2 |
-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-1 / Detector: PIXEL / Date: Nov 4, 2018 / Frequency: 120 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.33 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→32.43 Å / Num. obs: 29269 / % possible obs: 98.9 % / Redundancy: 61.8 % / CC star: 0.99 / R split: 0.264 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 12462 / CC star: 0.512 / R split: 5.14 / % possible all: 90.6 |
Serial crystallography measurement | Collection time total: 2 hours / Collimation: KB mirrors / Focal spot size: 2 µm2 / Pulse duration: 35 fsec. / Pulse energy: 0.1 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: LCP / Description: LCP injector / Flow rate: 0.44 µL/min / Injector diameter: 50 µm / Injector temperature: 293 K / Jet diameter: 50 µm / Power by: HPLC pump |
Serial crystallography data reduction | Crystal hits: 20358 / Frames total: 850000 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D27 Resolution: 2.61→32.43 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.54 Å2 / Biso mean: 52.3671 Å2 / Biso min: 10.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.61→32.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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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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