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- PDB-5jp4: Crystal structure of S. pombe Dcp1 in complex with the decapping ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jp4 | ||||||
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Title | Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC | ||||||
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![]() | PEPTIDE BINDING PROTEIN / EVH1 / complex / mRNA / decapping / Hydrolase | ||||||
Function / homology | ![]() mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / cytoplasmic stress granule / mRNA processing / RNA binding ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / meiotic cell cycle / P-body / cytoplasmic stress granule / mRNA processing / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wurm, J.P. / Sprangers, R. | ||||||
![]() | ![]() Title: The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface. Authors: Wurm, J.P. / Overbeck, J. / Sprangers, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | 56 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qklS 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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Unit cell |
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Components
#1: Protein | Mass: 15130.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dcp1, SPBC3B9.21 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 4212.566 Da / Num. of mol.: 1 / Fragment: UNP Residues 156-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPAC18G6.09c / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M NaCl, 100 mM NaCitrate pH 5-6 / PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→47.813 Å / Num. obs: 10434 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QKL Resolution: 2.043→47.813 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.043→47.813 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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