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Yorodumi- PDB-5jc3: Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jc3 | ||||||
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Title | Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned). | ||||||
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 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 / RNA helicase activity / RNA helicase / hydrolase activity / innate immune response / DNA 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 / RNA helicase activity / RNA helicase / hydrolase activity / 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: 2.6 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 | 5jc3.cif.gz | 305.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jc3.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/5jc3 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/5jc3 | HTTPS FTP |
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-Related structure data
Related structure data | 5jajC 5jb2C 5jbgC 5jbjC 5jc7C 5jcfC 5jchC 4gl2S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 297 - 988 / Label seq-ID: 4 - 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 Source: (gene. exp.) Gallus gallus (chicken) / Gene: MDA5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: D9N195 #2: RNA chain | Mass: 3176.948 Da / Num. of mol.: 4 / Mutation: 5' monophosphate / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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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 using an ...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 using an Amicon Ultra concentrator to around 10 mg/ml and 2 mM AMPPNP (adenosine 5prime-(beta,gamma-imido)triphosphate lithium salt hydrate) 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 55300 / % possible obs: 99.3 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.83 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1.73 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GL2 Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.875 / SU B: 13.362 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.056 / ESU R Free: 0.363 / 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: 57.742 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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