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- PDB-5jbj: Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jbj | ||||||
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Title | Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 A resolution | ||||||
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![]() | IMMUNE SYSTEM / Innate immune pattern recognition receptor / RIG-I like helicase / dsRNA dependent ATPase / zinc-containing CTD domain | ||||||
Function / homology | ![]() negative regulation of RIG-I signaling pathway / antiviral innate immune response / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / hydrolase activity / RNA helicase / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. / Uchikawa, E. / Lethier, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.4 KB | Display | ![]() |
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PDB format | ![]() | 117.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.5 KB | Display | ![]() |
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Full document | ![]() | 474.3 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jajC ![]() 5jb2SC ![]() 5jbgC ![]() 5jc3C ![]() 5jc7C ![]() 5jcfC ![]() 5jchC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77459.000 Da / Num. of mol.: 1 Mutation: GAMGGGS from tag replaces the N-terminal methionine Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: RNA chain | Mass: 3827.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA 5 prime mono phosphate / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 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. chLGP2:12bp dsRNA:ADP:AlF4 complex was mixed with reservoir buffer (0.1 M Bis-Tris propane pH 6.5, 0.05-0.1 M magnesium formate) in a 2:1 ratio |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3.58→78.02 Å / Num. obs: 10663 / % possible obs: 78.02 % / Redundancy: 11.51 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.74 |
Reflection shell | Resolution: 3.58→3.73 Å / Redundancy: 10.32 % / Rmerge(I) obs: 1.18 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JB2 Resolution: 3.58→78.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 59.059 / SU ML: 0.855 / Cross valid method: THROUGHOUT / ESU R Free: 0.86 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 202.316 Å2
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Refinement step | Cycle: LAST / Resolution: 3.58→78.02 Å
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Refine LS restraints |
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