+Open data
-Basic information
Entry | Database: PDB / ID: 4bru | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the yeast Dhh1-Edc3 complex | ||||||
Components |
| ||||||
Keywords | HYDROLASE / DECAPPING / TRANSLATIONAL REPRESSION / MRNP REMODEL P-BODY / DEAD-BOX | ||||||
Function / homology | Function and homology information invasive filamentous growth / regulation of cytoplasmic mRNA processing body assembly / response to pheromone triggering conjugation with cellular fusion / pseudohyphal growth / 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 / filamentous growth ...invasive filamentous growth / regulation of cytoplasmic mRNA processing body assembly / response to pheromone triggering conjugation with cellular fusion / pseudohyphal growth / 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 / filamentous growth / P-body assembly / cellular response to nitrogen starvation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA transport / cellular response to glucose starvation / stress granule assembly / positive regulation of translation / P-body / cytoplasmic stress granule / mRNA processing / 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 | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.245 Å | ||||||
Authors | Sharif, H. / Ozgur, S. / Sharma, K. / Basquin, C. / Urlaub, H. / Conti, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bru.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bru.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bru_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bru_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 4bru_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 4bru_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/4bru ftp://data.pdbj.org/pub/pdb/validation_reports/br/4bru | HTTPS FTP |
-Related structure data
Related structure data | 4brwC 1s2mS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P39517, RNA helicase |
---|---|
#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.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P39998 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.67 % / Description: NONE |
---|---|
Crystal grow | Details: 50 MM MES PH 6.0, 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97961 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|