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Yorodumi- PDB-6rz7: Crystal structure of the human cysteinyl leukotriene receptor 2 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rz7 | |||||||||||||||
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Title | Crystal structure of the human cysteinyl leukotriene receptor 2 in complex with ONO-2570366 (F222 space group) | |||||||||||||||
Components | Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / cyslt2 / cysltr2 / cyslt2r / asthma / BRIL / Cysteinyl Leukotriene Receptor 2 | |||||||||||||||
Function / homology | Function and homology information cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / electron transfer activity / periplasmic space ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / G protein-coupled peptide receptor activity / neuropeptide signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / electron transfer activity / periplasmic space / immune response / iron ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | |||||||||||||||
Authors | Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Fujimoto, T. / Maruyama, T. ...Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Fujimoto, T. / Maruyama, T. / Stauch, B. / Ergasheva, M. / Romanovskaya, D. / Stepko, A. / Kovalev, K. / Shevtsov, M. / Gordeliy, V. / Han, G.W. / Sarret, P. / Katritch, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V. | |||||||||||||||
Funding support | Russian Federation, United States, Canada, 4items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors. Authors: Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Patel, N. / Fujimoto, T. / Maruyama, T. / Stauch, B. / ...Authors: Gusach, A. / Luginina, A. / Marin, E. / Brouillette, R.L. / Besserer-Offroy, E. / Longpre, J.M. / Ishchenko, A. / Popov, P. / Patel, N. / Fujimoto, T. / Maruyama, T. / Stauch, B. / Ergasheva, M. / Romanovskaia, D. / Stepko, A. / Kovalev, K. / Shevtsov, M. / Gordeliy, V. / Han, G.W. / Katritch, V. / Borshchevskiy, V. / Sarret, P. / Mishin, A. / Cherezov, V. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rz7.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rz7.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6rz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rz7 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rz7 | HTTPS FTP |
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-Related structure data
Related structure data | 6rz6C 6rz8C 6rz9C 6rz4S 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: 45995.961 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: CYSLTR2, CYSLT2, CYSLT2R, PSEC0146, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NS75, UniProt: P0ABE7 |
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-Non-polymers , 6 types, 46 molecules
#2: Chemical | ChemComp-KNW / ( | ||||||
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#3: Chemical | ChemComp-CLR / | ||||||
#4: Chemical | #5: Chemical | ChemComp-OLA / #6: Chemical | ChemComp-PGE / | #7: 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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 30 mM NH4 tartrate dibasic 24% PEG400 100 mM HEPES 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.07228 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07228 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→20 Å / Num. obs: 17665 / % possible obs: 92.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.108 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 3.9 % / Rmerge(I) obs: 2.168 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.22 / Rpim(I) all: 1.192 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RZ4 Resolution: 2.43→19.93 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→19.93 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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