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Yorodumi- PDB-6fc3: Crystal structure of the eIF4E-p20 complex from Saccharomyces cer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fc3 | ||||||
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Title | Crystal structure of the eIF4E-p20 complex from Saccharomyces cerevisiae | ||||||
Components |
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Keywords | TRANSLATION / Translation Translational control Gene expression 4E-binding protein | ||||||
Function / homology | Function and homology information : / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / positive regulation of cytoplasmic mRNA processing body assembly / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding ...: / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / positive regulation of cytoplasmic mRNA processing body assembly / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translational initiation / translation initiation factor activity / cytoplasmic stress granule / negative regulation of translation / ribosome / regulation of cell cycle / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Gruener, S. / Valkov, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast. Authors: Gruner, S. / Weber, R. / Peter, D. / Chung, M.Y. / Igreja, C. / Valkov, E. / Izaurralde, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fc3.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fc3.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fc3_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 6fc3_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 6fc3_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6fc3_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fc3 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fc3 | HTTPS FTP |
-Related structure data
Related structure data | 6fbzSC 6fc0C 6fc1C 6fc2C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20806.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CDC33, TIF45, YOL139C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07260 | ||||
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#2: Protein | Mass: 6202.093 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CAF20, CAF2, CAP20, YOR276W, O5453W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12962 | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Na-acetate (pH 5.0) 13% (w/v) PEG 6000 10 mM ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.78 Å / Num. obs: 27294 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.114 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1510 / CC1/2: 0.454 / Rsym value: 1.056 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FBZ, chain A Resolution: 1.75→42.78 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→42.78 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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