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Yorodumi- PDB-4a2x: Structure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a2x | ||||||
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Title | Structure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / ANTIVIRAL SIGNALLING PATHWAY | ||||||
Function / homology | Function and homology information RNA helicase activity / hydrolase activity / RNA helicase / innate immune response / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ANAS PLATYRHYNCHOS (mallard) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Kowalinski, E. / Lunardi, T. / McCarthy, A.A. / Cusack, S. | ||||||
Citation | Journal: Cell / Year: 2011 Title: Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA. Authors: Kowalinski, E. / Lunardi, T. / McCarthy, A.A. / Louber, J. / Brunel, J. / Grigorov, B. / 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 | 4a2x.cif.gz | 279.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a2x.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/4a2x ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a2x | HTTPS FTP |
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-Related structure data
Related structure data | 4a2pC 4a2qC 4a2vSC 4a2wC 4a36C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper:
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-Components
#1: Protein | Mass: 15181.542 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 806-933 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANAS PLATYRHYNCHOS (mallard) / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: D3TI84 #2: RNA chain | Mass: 4587.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: RNA chain | Mass: 4352.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: Chemical | ChemComp-ZN / Sequence details | ADDITIONAL | |
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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: 3.92 Å3/Da / Density % sol: 61.5 % / Description: NONE |
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Crystal grow | Details: 14 MG/ML IN A 2:1 MOLAR RATIO WITH 14-MER DSRNA AND 0.1 M TRIS PH 8.8, 26% (W/V) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 10316 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.47 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 4→4.2 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / % possible all: 94 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A2V Resolution: 4→108.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 94.5 / SU ML: 0.553 / Cross valid method: THROUGHOUT / ESU R Free: 0.733 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 68.041 Å2
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Refinement step | Cycle: LAST / Resolution: 4→108.01 Å
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Refine LS restraints |
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