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- PDB-2v8y: Crystallographic and mass spectrometric characterisation of eIF4E... -
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Basic information
Entry | Database: PDB / ID: 2v8y | ||||||
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Title | Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives | ||||||
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![]() | TRANSLATION / PHOSPHORYLATION / INITIATION FACTOR / CAP / EIF4E / 7BNGMP / 4E-BP1 / RNA-BINDING / ACETYLATION / HOST-VIRUS INTERACTION / PROTEIN SYNTHESIS INHIBITOR / PROTEIN BIOSYNTHESIS / TRANSLATION REGULATION | ||||||
Function / homology | ![]() Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Deadenylation of mRNA / mRNA cap binding ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Deadenylation of mRNA / mRNA cap binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / stem cell population maintenance / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / TOR signaling / behavioral fear response / mRNA export from nucleus / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brown, C.J. / Mcnae, I. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: Crystallographic and Mass Spectrometric Characterisation of Eif4E with N(7)-Alkylated CAP Derivatives. Authors: Brown, C.J. / Mcnae, I. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 103.1 KB | Display | ![]() |
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PDB format | ![]() | 78.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v8wC ![]() 2v8xC ![]() 1ejhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 25130.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1861.240 Da / Num. of mol.: 2 / Fragment: PHAS-I4E-BP1 BINDING PEPTIDE, RESIDUES 50-63 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % / Description: NONE |
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Crystal grow | pH: 7 Details: 25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.17 Å / Num. obs: 28510 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 87.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EJH Resolution: 2.1→25.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.956 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25.3 Å
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