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Open data
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Basic information
Entry | Database: PDB / ID: 5aby | |||||||||
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Title | Complex of C. elegans eIF4E-3 with the 4E-binding protein Mextli | |||||||||
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![]() | TRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN | |||||||||
Function / homology | ![]() translation initiation complex / L13a-mediated translational silencing of Ceruloplasmin expression / : / : / : / Translation initiation complex formation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Ribosomal scanning and start codon recognition / regulation of formation of translation initiation ternary complex / ISG15 antiviral mechanism ...translation initiation complex / L13a-mediated translational silencing of Ceruloplasmin expression / : / : / : / Translation initiation complex formation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Ribosomal scanning and start codon recognition / regulation of formation of translation initiation ternary complex / ISG15 antiviral mechanism / 21U-RNA metabolic process / RNA cap binding complex / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / regulatory ncRNA-mediated gene silencing / RNA 7-methylguanosine cap binding / embryo development ending in birth or egg hatching / translational initiation / translation initiation factor activity / positive regulation of translation / perinuclear region of cytoplasm / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Peter, D. / Weichenrieder, O. | |||||||||
![]() | ![]() Title: Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form Eif4E Complexes that Display Differential Sensitivity to 4E-BP Regulation Authors: Peter, D. / Weber, R. / Koene, C. / Chung, M.-Y. / Ebertsch, L. / Truffault, V. / Weichenrieder, O. / Igreja, C. / Izaurralde, E. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.4 KB | Display | ![]() |
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PDB format | ![]() | 224.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
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Full document | ![]() | 475.6 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5abuC ![]() 5abvC ![]() 5abxSC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22377.488 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 30-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 4740.511 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 471-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE FIRST FOUR RESIDUES OF CHAINS A, C, E REMAIN FROM THE EXPRESSION TAG. THE FIRST FOUR RESIDUES ...THE FIRST FOUR RESIDUES OF CHAINS A, C, E REMAIN FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M TRIS, PH=8.0, 0.2M MGCL2, 17% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.2 Å / Num. obs: 58918 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 29.49 Å2 / Rsym value: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2 / Rsym value: 1.17 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5ABX Resolution: 1.95→45.522 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 20.91 / Stereochemistry target values: ML Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 203 TO 209. CHAIN C, RESIDUES 203 TO 208. CHAIN E, RESIDUES 202 TO 209. CHAIN F, RESIDUE 507.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.522 Å
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Refine LS restraints |
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LS refinement shell |
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