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Open data
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Basic information
Entry | Database: PDB / ID: 4bru | ||||||
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Title | Crystal structure of the yeast Dhh1-Edc3 complex | ||||||
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![]() | HYDROLASE / DECAPPING / TRANSLATIONAL REPRESSION / MRNP REMODEL P-BODY / DEAD-BOX | ||||||
Function / homology | ![]() regulation of cytoplasmic mRNA processing body assembly / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA transport / stress granule assembly ...regulation of cytoplasmic mRNA processing body assembly / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA transport / stress granule assembly / positive regulation of translation / P-body / mRNA processing / cytoplasmic stress granule / RNA helicase activity / negative regulation of translation / RNA helicase / mRNA binding / chromatin binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharif, H. / Ozgur, S. / Sharma, K. / Basquin, C. / Urlaub, H. / Conti, E. | ||||||
![]() | ![]() Title: Structural Analysis of the Yeast Dhh1-Pat1 Complex Reveals How Dhh1 Engages Pat1, Edc3 and RNA in Mutually Exclusive Interactions Authors: Sharif, H. / Ozgur, S. / Sharma, K. / Basquin, C. / Urlaub, H. / Conti, E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.1 KB | Display | ![]() |
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PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4brwC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 42840.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-422 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 5326.702 Da / Num. of mol.: 1 / Fragment: RESIDUES 77-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.67 % / Description: NONE |
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Crystal grow | Details: 50 MM MES PH 6.0, 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→53.7 Å / Num. obs: 11718 / % possible obs: 99.7 % / Redundancy: 17.3 % / Biso Wilson estimate: 111.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 3.25→3.36 Å / Redundancy: 16 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S2M Resolution: 3.245→53.704 Å / SU ML: 0.45 / σ(F): 2.02 / Phase error: 26.1 / Stereochemistry target values: ML Details: RESIDUE CHAIN A 422 NOT MODELED. RESIDUES CHAIN B 77-87 DISORDERED
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.245→53.704 Å
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Refine LS restraints |
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LS refinement shell |
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