+Open data
-Basic information
Entry | Database: PDB / ID: 2jgb | ||||||
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Title | Structure of human eIF4E homologous protein 4EHP with m7GTP | ||||||
Components |
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Keywords | TRANSLATION / PHOSPHORYLATION / INITIATION FACTOR / 4EHP / EIF4E / RNA-BINDING / ACETYLATION / CAP-BINDING / EUKARYOTIC INITIATION FACTOR / PROTEIN SYNTHESIS INHIBITOR / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION | ||||||
Function / homology | Function and homology information Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / negative regulation of type I interferon-mediated signaling pathway / TOR signaling / mTORC1-mediated signalling / rescue of stalled ribosome / translation initiation factor binding / translation repressor activity / negative regulation of translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / negative regulation of translation / ubiquitin protein ligase binding / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cameron, A.D. / Rosettani, P. / Knapp, S. / Vismara, M.G. / Rusconi, L. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2007 Title: Structures of the human eIF4E homologous protein, h4EHP, in its m7GTP-bound and unliganded forms. Authors: Rosettani, P. / Knapp, S. / Vismara, M.G. / Rusconi, L. / Cameron, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgb.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgb.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgb ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgb | HTTPS FTP |
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-Related structure data
Related structure data | 2jgcC 1ipbS 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
#1: Protein | Mass: 22499.787 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60573 |
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#2: Protein/peptide | Mass: 2144.564 Da / Num. of mol.: 1 / Fragment: RESIDUES 50-66 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q13541 |
#3: Chemical | ChemComp-MGT / |
#4: Water | ChemComp-HOH / |
Sequence details | THE INITIAL GPLHM HAS BEEN INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5 WITH 1MM M7GTP IN THE DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 26, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 111967 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IPB Resolution: 1.7→51.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.315 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 225 TO 227 OF THE PROTEIN CANNOT BE OBSERVED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→51.92 Å
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