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- PDB-5jch: Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jch | ||||||
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Title | Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.95 A resolution (untwinned). | ||||||
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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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 303.7 KB | Display | ![]() |
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PDB format | ![]() | 237.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1005.1 KB | Display | ![]() |
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Full document | ![]() | 1013.6 KB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jajC ![]() 5jb2C ![]() 5jbgC ![]() 5jbjC ![]() 5jc3SC ![]() 5jc7C ![]() 5jcfC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 298 - 988 / Label seq-ID: 5 - 695
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Components
#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 and CTD domains / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 3176.948 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Synthetic dsRNA obtained by in vitro T7 transcription Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Directly after size exclusion chromatography chMDA5 deltaCARD-Q was mixed with 10 bp dsRNA in a 1:1 molar ratio and incubated for 30 minutes on ice. The complex was concentrated to around 10 ...Details: Directly after size exclusion chromatography chMDA5 deltaCARD-Q was mixed with 10 bp dsRNA in a 1:1 molar ratio and incubated for 30 minutes on ice. The complex was concentrated to around 10 mg/ml and 2 mM AMPPNP was added. Sample and reservoir buffer (0.025 M Bis-Tris pH 6.5, 0.075 M succinic acid pH 7.0, 12-14% PEG 3350, 2% sucrose) were mixed in a 2:1 ratio. Three hours after setup, cover glasses with drops were transferred from a reservoir containing 12-14% PEG 3350 to one containing 8% PEG 3350. Crystals grew in one week at 20 C and were harvested in cryo-protectant solution (0.025 M Bis-Tris pH 6.5, 0.075 M succinic acid pH 7.0, 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: Feb 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 38060 / % possible obs: 94 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.94 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 1.78 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JC3 Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.908 / SU B: 30.813 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / 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: 81.287 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→50 Å
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Refine LS restraints |
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