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Yorodumi- PDB-6rz4: Crystal structure of cysteinyl leukotriene receptor 1 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rz4 | ||||||||||||
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Title | Crystal structure of cysteinyl leukotriene receptor 1 in complex with pranlukast | ||||||||||||
Components | Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1 | ||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / LTD4 / cyslt1 / cysltr1 / cyslt1r asthma / pranlukast / BRIL / sodium site / Cysteinyl Leukotriene Receptor 1 | ||||||||||||
Function / homology | Function and homology information cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / respiratory gaseous exchange by respiratory system / G protein-coupled peptide receptor activity / inflammatory response to antigenic stimulus / neuropeptide signaling pathway / establishment of localization in cell / electron transport chain ...cysteinyl leukotriene receptor activity / leukotriene receptor activity / Leukotriene receptors / LTC4-CYSLTR mediated IL4 production / respiratory gaseous exchange by respiratory system / G protein-coupled peptide receptor activity / inflammatory response to antigenic stimulus / neuropeptide signaling pathway / establishment of localization in cell / electron transport chain / defense response / chemotaxis / calcium ion transport / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / Potential therapeutics for SARS / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / iron ion binding / heme binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Luginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiryaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. ...Luginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiryaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. / Ishchenko, A. / Patel, N. / Polovinkin, V. / Safronova, N. / Bogorodskiy, A. / Edelweiss, E. / Liu, W. / Batyuk, A. / Gordeliy, V. / Han, G.W. / Sarret, P. / Katritch, V. / Borshchevskiy, V. / Cherezov, V. | ||||||||||||
Funding support | Russian Federation, United States, Canada, 3items
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Citation | Journal: Sci Adv / Year: 2019 Title: Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs. Authors: Luginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiriaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. / Ishchenko, A. / Patel, N. / Polovinkin, ...Authors: Luginina, A. / Gusach, A. / Marin, E. / Mishin, A. / Brouillette, R. / Popov, P. / Shiriaeva, A. / Besserer-Offroy, E. / Longpre, J.M. / Lyapina, E. / Ishchenko, A. / Patel, N. / Polovinkin, V. / Safronova, N. / Bogorodskiy, A. / Edelweiss, E. / Hu, H. / Weierstall, U. / Liu, W. / Batyuk, A. / Gordeliy, V. / Han, G.W. / Sarret, P. / Katritch, V. / Borshchevskiy, V. / Cherezov, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rz4.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rz4.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rz4 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rz4 | HTTPS FTP |
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-Related structure data
Related structure data | 6rz5C 4eiyS 4xnwS 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: 47927.090 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: CYSLTR1, CYSLT1, cybC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y271, UniProt: P0ABE7 |
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-Non-polymers , 5 types, 28 molecules
#2: Chemical | ChemComp-KNT / | ||||
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#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-OLC / ( #5: Chemical | ChemComp-OLA / | #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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: crystals had a twiggy shape |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 100 mM sodium citrate pH 6 200-600 mM lithium nitrate 30-38% v/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 12749 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.269 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1278 / CC1/2: 0.642 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XNW,4EIY Resolution: 2.7→29.3 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.832 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 2.308 / SU Rfree Blow DPI: 0.333
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Displacement parameters | Biso mean: 65.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.96 Å / Total num. of bins used: 6
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