[English] 日本語
Yorodumi- PDB-6rz5: XFEL crystal structure of the human cysteinyl leukotriene recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rz5 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | XFEL crystal structure of the human cysteinyl leukotriene receptor 1 in complex with zafirlukast | ||||||||||||
Components | Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1 | ||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / LCP / cysteinyl leukotriene / LTD4 / cyslt1 / cysltr1 / cyslt1r / asthma / zafirlukast / BRIL / sodium site / Cysteinyl Leukotriene Receptor 1 / XFEL / Serial Femtosecond Crystallography / SFX | ||||||||||||
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 / Potential therapeutics for SARS / G alpha (q) signalling events / periplasmic space / cell surface receptor signaling pathway / electron transfer activity / iron ion binding / heme 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 / Resolution: 2.53 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
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rz5.cif.gz | 331 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rz5.ent.gz | 264 KB | Display | PDB format |
PDBx/mmJSON format | 6rz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rz5_validation.pdf.gz | 6.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rz5_full_validation.pdf.gz | 6.9 MB | Display | |
Data in XML | 6rz5_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 6rz5_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rz5 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rz5 | HTTPS FTP |
-Related structure data
Related structure data | 6rz4SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1660939 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47927.090 Da / Num. of mol.: 2 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 |
---|
-Non-polymers , 6 types, 52 molecules
#2: Chemical | #3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-OLA / #5: Chemical | ChemComp-1PE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 75-175 mM sodium phosphate 24-34% v/v PEG400 100 mM HEPES pH 7.0 1 uM zafirlukast |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.302 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 21, 2016 / Details: pair of Kirkpatrick-Baez mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.302 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→20 Å / Num. obs: 30258 / % possible obs: 100 % / Redundancy: 82.7 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.98 / R split: 0.2 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 43.2 % / Num. unique obs: 2988 / CC1/2: 0.2 / R split: 2.19 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 2.25 µm2 / Pulse duration: 43 fsec. / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: LCP jet / Method: injection |
Serial crystallography sample delivery injection | Description: LCP jet / Flow rate: 0.2 µL/min / Injector diameter: 50 µm |
Serial crystallography data reduction | Crystal hits: 40720 / Frames indexed: 30129 / Frames total: 315374 / Lattices indexed: 32568 / XFEL pulse events: 315374 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RZ4 Resolution: 2.53→19.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.415 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.255
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→19.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.53→2.55 Å / Total num. of bins used: 50
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|