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Open data
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Basic information
Entry | Database: PDB / ID: 5eir | ||||||
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Title | Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. | ||||||
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![]() | TRANSLATION / Complex / inhibitor / eIF4E | ||||||
Function / homology | ![]() positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / regulation of cellular response to stress / eukaryotic initiation factor 4E binding / regulation of translation at postsynapse, modulating synaptic transmission ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic initiation factor 4G binding / regulation of cellular response to stress / 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 / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / Transport of the SLBP independent Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of protein localization to cell periphery / RISC complex / regulation of translational initiation / Translation initiation complex formation / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / cellular response to nutrient levels / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / regulation of presynapse assembly / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / behavioral fear response / positive regulation of G1/S transition of mitotic cell cycle / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / energy homeostasis / translation initiation factor binding / translational initiation / positive regulation of protein metabolic process / translation initiation factor activity / positive regulation of neuron differentiation / negative regulation of autophagy / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / AUF1 (hnRNP D0) binds and destabilizes mRNA / lung development / P-body / neuron differentiation / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / positive regulation of peptidyl-serine phosphorylation / regulation of translation / positive regulation of cell growth / postsynapse / DNA-binding transcription factor binding / response to ethanol / molecular adaptor activity / negative regulation of translation / ribosome / nuclear speck / translation / mRNA binding / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nowicki, M.W. / Walkinshaw, M.D. / Fischer, P.M. | ||||||
![]() | ![]() Title: Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation. Authors: Soukarieh, F. / Nowicki, M.W. / Bastide, A. / Poyry, T. / Jones, C. / Dudek, K. / Patwardhan, G. / Meullenet, F. / Oldham, N.J. / Walkinshaw, M.D. / Willis, A.E. / Fischer, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
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PDB format | ![]() | 42.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ehcC ![]() 5ei3C ![]() 5ekvC ![]() 2v8yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25130.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1851.155 Da / Num. of mol.: 1 / Fragment: eIF4E binding sequence / Source method: obtained synthetically / Details: commercial synthesis / Source: (synth.) synthetic construct (others) / References: UniProt: Q04637*PLUS |
#3: Chemical | ChemComp-5O8 / ~{ |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding. Crystals replaced in to above conditions without (NH4)2SO4 prior to freezing. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 15, 2011 / Details: PILATUS 6M | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→123.67 Å / Num. all: 6814 / Num. obs: 6814 / % possible obs: 93.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 22.08 Å2 / Rpim(I) all: 0.106 / Rrim(I) all: 0.193 / Rsym value: 0.16 / Net I/av σ(I): 3.5 / Net I/σ(I): 5.5 / Num. measured all: 19790 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V8Y chain A Resolution: 2.69→48.029 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 0.29 / Phase error: 25.73 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 97.52 Å2 / Biso mean: 25.137 Å2 / Biso min: 3.64 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.69→48.029 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 92 %
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