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Yorodumi- PDB-5jbg: Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jbg | ||||||
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Title | Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and ADP-AlF4-Mg2+ at 2.0 A resolution. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Innate immune pattern recognition receptor / RIG-I like helicase / dsRNA dependent ATPase / zinc-containing CTD domain | ||||||
Function / homology | Function and homology information RNA helicase activity / hydrolase activity / RNA helicase / innate immune response / DNA binding / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cusack, S. / Uchikawa, E. | ||||||
Funding support | France, 1items
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Citation | Journal: Mol.Cell / Year: 2016 Title: Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5. Authors: Uchikawa, E. / Lethier, M. / Malet, H. / Brunel, J. / Gerlier, D. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jbg.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jbg.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jbg ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jbg | HTTPS FTP |
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-Related structure data
Related structure data | 5jajC 5jb2SC 5jbjC 5jc3C 5jc7C 5jcfC 5jchC 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 / RNA chain , 2 types, 2 molecules AX
#1: Protein | Mass: 77459.000 Da / Num. of mol.: 1 / Mutation: GAMGGGS from tag replaces N-terminal methionine Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0YYQ5 |
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#2: RNA chain | Mass: 8565.016 Da / Num. of mol.: 1 / Mutation: 5' triphosphate / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 277 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-ADP / | ||
#5: Chemical | ChemComp-ALF / | ||
#6: Chemical | ChemComp-MG / | ||
#7: Chemical | ChemComp-SO4 / #8: 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: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator ...Details: chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added. 5 prime triphosphate, 3 prime GG overhang 26-mer hairpin RNA:ADP:AlF4 complex was mixed with reservoir buffer containing 0.1 M citric acid pH 5.0, 0.8 M ammonium sulphate in a 1:1 ratio. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.27 Å / Num. obs: 56661 / % possible obs: 99.9 % / Redundancy: 4.47 % / Rmerge(I) obs: 0.259 / Net I/σ(I): 6.31 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.38 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JB2 Resolution: 2→76.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.593 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.664 Å2
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Refinement step | Cycle: 1 / Resolution: 2→76.27 Å
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Refine LS restraints |
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