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Yorodumi- PDB-1l8b: Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l8b | ||||||
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Title | Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to 7-methylGpppG | ||||||
Components | EUKARYOTIC TRANSLATION INITIATION FACTOR 4EEIF4E | ||||||
Keywords | RNA BINDING PROTEIN / eukaryotic initiation factor 4E / eIF4E / cap / 7-methylGpppG | ||||||
Function / homology | Function and homology information Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / mTORC1-mediated signalling / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / : / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Niedzwiecka, A. / Marcotrigiano, J. / Stepinski, J. / Jankowska-Anyszka, M. / Wyslouch-Cieszynska, A. / Dadlez, M. / Gingras, A.-C. / Mak, P. / Darzynkiewicz, E. / Sonenberg, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5' cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins. Authors: Niedzwiecka, A. / Marcotrigiano, J. / Stepinski, J. / Jankowska-Anyszka, M. / Wyslouch-Cieszynska, A. / Dadlez, M. / Gingras, A.C. / Mak, P. / Darzynkiewicz, E. / Sonenberg, N. / Burley, S.K. / Stolarski, R. | ||||||
History |
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Remark 600 | HETEROGEN THE 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE (MGP) IS ACTUALLY BOUND TO ANOTHER GUANOSINE-5'- ...HETEROGEN THE 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE (MGP) IS ACTUALLY BOUND TO ANOTHER GUANOSINE-5'-MONOPHOSPHATE, WHICH IS MISSING IN THE ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8b.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8b.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8b ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22145.113 Da / Num. of mol.: 2 / Fragment: residues 28-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63073 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.4 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Marcotrigiano, J., (1997) Cell, 89, 951. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Dec 4, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 38968 / % possible obs: 97.8 % / Observed criterion σ(I): 4 / Redundancy: 7 % / Rsym value: 0.103 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 4 % / Rsym value: 0.259 / % possible all: 87.5 |
Reflection | *PLUS Rmerge(I) obs: 0.103 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å /
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Refinement | *PLUS Rfactor obs: 0.224 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.224 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.238 / Rfactor Rwork: 0.211 / Rfactor obs: 0.211 |