+Open data
-Basic information
Entry | Database: PDB / ID: 4ct5 | ||||||
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Title | DDX6 | ||||||
Components | DDX6 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body ...mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / negative regulation of translation / RNA helicase activity / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ozgur, S. / Basquin, J. / Conti, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression. Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ct5.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ct5.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ct5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/4ct5 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/4ct5 | HTTPS FTP |
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-Related structure data
Related structure data | 4ct4C 4ct6C 4ct7C 4cv5C 2waxS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43189.195 Da / Num. of mol.: 2 / Fragment: RECA1, RECA2, RESIDUES 95-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PRARE / References: UniProt: P26196, RNA helicase #2: Chemical | Sequence details | THE FIRST 3 AMINO ACIDS ARE FROM THE PROTEASE CLEAVAGE SITE (RSM) | |
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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 17% (W/V) PEG 10000, 100 MM BIS-TRIS PH 5.5 AND 100 MM AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 3→80 Å / Num. obs: 27769 / % possible obs: 99.4 % / Observed criterion σ(I): 2.4 / Redundancy: 5.2 % / Biso Wilson estimate: 81.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3→3.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WAX Resolution: 3→50.59 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→50.59 Å
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Refine LS restraints |
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LS refinement shell |
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