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Yorodumi- PDB-5abv: Complex of D. melanogaster eIF4E with the 4E-binding protein Mextli -
+Open data
-Basic information
Entry | Database: PDB / ID: 5abv | ||||||
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Title | Complex of D. melanogaster eIF4E with the 4E-binding protein Mextli | ||||||
Components |
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Keywords | TRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN | ||||||
Function / homology | Function and homology information regulation of formation of translation initiation ternary complex / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / : / female germ-line stem cell population maintenance / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / mTORC1-mediated signalling ...regulation of formation of translation initiation ternary complex / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / : / female germ-line stem cell population maintenance / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / mTORC1-mediated signalling / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / muscle cell postsynaptic specialization / trans-synaptic signaling / RNA cap binding complex / neuronal ribonucleoprotein granule / RNA metabolic process / messenger ribonucleoprotein complex / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translational initiation / translation initiation factor activity / positive regulation of translation / P-body / neuromuscular junction / postsynapse / nuclear body / translation / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Peter, D. / Weichenrieder, O. | ||||||
Citation | Journal: Genes Dev. / Year: 2015 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5abv.cif.gz | 402.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5abv.ent.gz | 334.6 KB | Display | PDB format |
PDBx/mmJSON format | 5abv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5abv ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abv | HTTPS FTP |
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-Related structure data
Related structure data | 5abuC 5abxC 5abyC 4ue8S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21249.037 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 69-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598 #2: Protein | Mass: 8225.225 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 577-640 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9VR35 #3: Water | ChemComp-HOH / | Sequence details | NUMBERING OF CHAIN A, C, E, G CORRESPONDS TO UNP P48598-2. COMPARED TO UNP P48598, SEQUENCE NUMBERS ...NUMBERING OF CHAIN A, C, E, G CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.1M BISTRIS PH=6.0, 23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→44 Å / Num. obs: 50587 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 45.69 Å2 / Rsym value: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.44 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UE8 CHAIN A Resolution: 2.13→43.96 Å / Cor.coef. Fo:Fc: 0.9479 / Cor.coef. Fo:Fc free: 0.9228 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.198 Details: REFINEMENT WAS DONE WITH ONE TLS GROUP PER CHAIN AND BUSTER AUTO NCS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 238 TO 240. CHAIN B, RESIDUES 639, 640. CHAIN C, RESIDUES ...Details: REFINEMENT WAS DONE WITH ONE TLS GROUP PER CHAIN AND BUSTER AUTO NCS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 238 TO 240. CHAIN B, RESIDUES 639, 640. CHAIN C, RESIDUES 151,152,189,190,238 TO 241. CHAIN D, RESIDUES 638 TO 640. CHAIN E, RESIDUES 238 TO 240. CHAIN F, RESIDUES 636 TO 640. CHAIN G, RESIDUES 220, 221, 237 TO 240. CHAIN H, RESIDUES 637 TO 640. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 65.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→43.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.19 Å / Total num. of bins used: 20
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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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