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Yorodumi- PDB-2jgc: Structure of the human eIF4E homologous protein, 4EHP without lig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jgc | ||||||
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Title | Structure of the human eIF4E homologous protein, 4EHP without ligand bound | ||||||
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 / mTORC1-mediated signalling ...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 / mTORC1-mediated signalling / TOR signaling / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / positive regulation of mitotic cell cycle / rescue of stalled ribosome / translational initiation / P-body / ISG15 antiviral mechanism / G1/S transition of mitotic cell cycle / 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: 2.4 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 | 2jgc.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgc.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jgc_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
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Full document | 2jgc_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 2jgc_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2jgc_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgc ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgc | HTTPS FTP |
-Related structure data
Related structure data | 2jgbSC 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: 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 |
-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: Oct 5, 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: 2.4→28 Å / Num. obs: 34849 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JGB Resolution: 2.4→51.71 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.679 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 44-46, 72-79 AND 220-227 ARE DISORDERED
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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: 26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→51.71 Å
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