+Open data
-Basic information
Entry | Database: PDB / ID: 4aza | ||||||
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Title | Improved eIF4E binding peptides by phage display guided design. | ||||||
Components |
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Keywords | TRANSLATION | ||||||
Function / homology | Function and homology information 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 / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / 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 / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / mRNA cap binding / : / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of protein localization to cell periphery / RISC complex / regulation of translational initiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / cellular response to nutrient levels / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / translation initiation factor binding / energy homeostasis / translational initiation / translation initiation factor activity / positive regulation of protein metabolic process / positive regulation of neuron differentiation / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / negative regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / P-body / lung development / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / regulation of translation / positive regulation of peptidyl-serine phosphorylation / postsynapse / positive regulation of cell growth / response to ethanol / DNA-binding transcription factor binding / negative regulation of translation / molecular adaptor activity / ribosome / nuclear speck / translation / mRNA binding / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Chew, W.Z. / Quah, S.T. / Verma, C.S. / Liu, Y. / Lane, D.P. / Brown, C.J. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Improved Eif4E Binding Peptides by Phage Display Guided Design: Plasticity of Interacting Surfaces Yield Collective Effects. Authors: Zhou, W. / Quah, S.T. / Verma, C.S. / Liu, Y. / Lane, D.P. / Brown, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aza.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aza.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 4aza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4aza ftp://data.pdbj.org/pub/pdb/validation_reports/az/4aza | HTTPS FTP |
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-Related structure data
Related structure data | 2w97S S: Starting model for refinement |
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Similar structure data |
-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: 25130.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06730 #2: Protein/peptide | Mass: 1571.888 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: N-TERMINAL IS ACETYLATED AND C-TERMINAL IS AMIDATED. Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q04637*PLUS #3: Chemical | #4: 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: 2.89 Å3/Da / Density % sol: 57.42 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 20% PEG 5000 MME, 100 MM BISTRIS PH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PROTEUM / Wavelength: 1.5418 |
Detector | Type: RIGAKU PT 135 / Detector: CCD / Date: Apr 1, 2012 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→60.88 Å / Num. obs: 30410 / % possible obs: 99.3 % / Observed criterion σ(I): 8 / Redundancy: 9.22 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.22 |
Reflection shell | Resolution: 2.16→2.26 Å / Redundancy: 6.51 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.38 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W97 Resolution: 2.16→121.76 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.849 / SU B: 6.491 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.217 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.461 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→121.76 Å
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