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- PDB-2way: Structure of the human DDX6 C-terminal domain in complex with an ... -
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Basic information
Entry | Database: PDB / ID: 2way | ||||||
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Title | Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide | ||||||
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![]() | HYDROLASE / DEAD-BOX PROTEIN / NUCLEOTIDE-BINDING / P54 / RCK / MIRNA / P-BODIES / HELICASE / DECAPPING / RNA-BINDING / PROTO-ONCOGENE / PHOSPHOPROTEIN / CHROMOSOMAL REARRANGEMENT / ATP-DEPENDENT RNA HELICASE / CYTOPLASM / MRNA DECAY / ATP-BINDING | ||||||
Function / homology | ![]() deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity ...deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / P-body assembly / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / neuron differentiation / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tritschler, F. / Weichenrieder, O. | ||||||
![]() | ![]() Title: Structural Basis for the Mutually Exclusive Anchoring of P Body Components Edc3 and Tral to the Dead Box Protein Ddx6/Me31B. Authors: Tritschler, F. / Braun, J.E. / Eulalio, A. / Truffault, V. / Izaurralde, E. / Weichenrieder, O. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2waxC ![]() 1s2mS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22475.650 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 296-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P26196, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Protein/peptide | Mass: 5069.437 Da / Num. of mol.: 2 / Fragment: FDF PEPTIDE, RESIDUES 192-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 % / Description: NONE |
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Crystal grow | Details: 0.04 M KH2PO4, 16% PEG 8000, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 19, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.5 Å / Num. obs: 17392 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S2M Resolution: 2.3→45.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES A 383-387, A 413-419, A 461-472, B 192-198, B 225-228, C 296, C 383-389, C 413-419, C 463-472, D 192-195, D 226--228 ARE DISORDERED
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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: 33.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.5 Å
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Refine LS restraints |
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