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- PDB-5jc7: Crystal structure of chicken MDA5 with 5'p 24-mer dsRNA and ADP-M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jc7 | ||||||
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Title | Crystal structure of chicken MDA5 with 5'p 24-mer dsRNA and ADP-Mg2+ at 2.75 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 | ![]() Caspase-8 and -10 mediated induction of NF-kB / RLR (RIG-like receptor) mediated induction of IFN alpha/beta / TRAF mediated activation of IRF / Negative Regulation of MDA5 signaling / TRAF6 mediated NF-kB activation / MDA-5 signaling pathway / antiviral innate immune response / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding ...Caspase-8 and -10 mediated induction of NF-kB / RLR (RIG-like receptor) mediated induction of IFN alpha/beta / TRAF mediated activation of IRF / Negative Regulation of MDA5 signaling / TRAF6 mediated NF-kB activation / MDA-5 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. | ||||||
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 | ![]() | 302.1 KB | Display | ![]() |
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PDB format | ![]() | 237.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1012.6 KB | Display | ![]() |
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Full document | ![]() | 1021.8 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 62.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jajC ![]() 5jb2C ![]() 5jbgC ![]() 5jbjC ![]() 5jc3SC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 81667.008 Da / Num. of mol.: 2 Mutation: N-terminal deletion of 1-297; GAMG from tag at N-terminus; C-terminal deletion of 995-1001; Point mutation E436Q. Source method: isolated from a genetically manipulated source Details: Chicken MDA5 helicase-CTD domains / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-RNA chain , 2 types, 2 molecules XY
#2: RNA chain | Mass: 8004.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic dsRNA using T7 polymerase / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 7699.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic dsRNA using T7 polymerase / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 6 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#4: Chemical | #5: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Directly after size exclusion chromatography chMDA5 deltaCARD-Q was mixed with 24-mer dsRNA in a 0.5:1 molar ratio and incubated for 30 minutes on ice. The complexes were concentrated to ...Details: Directly after size exclusion chromatography chMDA5 deltaCARD-Q was mixed with 24-mer dsRNA in a 0.5:1 molar ratio and incubated for 30 minutes on ice. The complexes were concentrated to around 10 mg/ml and 2 mM AMPPNP and 200 mM NDSB211 (Dimethyl(2-hydroxyethyl)ammonium propane sulfonate) were added. chMDA5 delatCARD-Q:24bp dsRNA:AMPPNP was mixed with reservoir buffer (0.1 mM Hepes pH 7.5, 11-12% PEG 3350, 2-4% sucrose) in a 2:1 ratio. Crystals grew in three days at 20 degree and were harvested in cryo-protecting solution (0.1 mM Hepes pH 7.5, 25% 3350, 10% ethylene glycol) before flash freezing with liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 48273 / % possible obs: 99.1 % / Redundancy: 4.66 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.58 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.52 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JC3 Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 34.451 / SU ML: 0.59 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / 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: 69.662 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→50 Å
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Refine LS restraints |
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