+Open data
-Basic information
Entry | Database: PDB / ID: 4brw | ||||||
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Title | Crystal structure of the yeast Dhh1-Pat1 complex | ||||||
Components |
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Keywords | HYDROLASE / TRANSLATIONAL REPRESSION / MRNP REMODELING / P- BOD | ||||||
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 / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / cytoplasmic side of membrane / negative regulation of translational elongation / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex ...invasive filamentous growth / regulation of cytoplasmic mRNA processing body assembly / response to pheromone triggering conjugation with cellular fusion / pseudohyphal growth / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / cytoplasmic side of membrane / negative regulation of translational elongation / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / filamentous growth / P-body assembly / cellular response to nitrogen starvation / regulation of translational initiation / mRNA transport / cellular response to glucose starvation / stress granule assembly / negative regulation of translational initiation / positive regulation of translation / P-body / kinetochore / cytoplasmic stress granule / mRNA processing / cytosolic small ribosomal subunit / RNA helicase activity / negative regulation of translation / RNA helicase / cell division / chromatin binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4brw.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4brw.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 4brw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4brw_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
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Full document | 4brw_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 4brw_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4brw_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/4brw ftp://data.pdbj.org/pub/pdb/validation_reports/br/4brw | HTTPS FTP |
-Related structure data
Related structure data | 4bruC 1s2mS 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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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.) 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 |
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#2: Protein | Mass: 7912.046 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 5-79 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: P25644, RNA helicase |
#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-1PE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.74 % / Description: NONE |
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Crystal grow | Details: 50 MM TRIS PH 8.0, 4% MPD, 200 MM NACL, 25% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97139 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97139 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→79.88 Å / Num. obs: 17668 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 73.29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S2M Resolution: 2.795→48.474 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.94 / Stereochemistry target values: ML / Details: DISORDERED CHAIN B RESIDUES 5-24, 55-79
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.795→48.474 Å
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Refine LS restraints |
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LS refinement shell |
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