+Open data
-Basic information
Entry | Database: PDB / ID: 5zk9 | ||||||
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Title | Stapled-peptides tailored against initiation of translation | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Cap dependent Translation | ||||||
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 4G binding / 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 / mRNA cap binding / : / Deadenylation of mRNA ...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 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 / mRNA cap binding / : / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / stem cell population maintenance / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / ISG15 antiviral mechanism / neuron differentiation / cytoplasmic stress granule / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Lama, D. / Liberator, A. / Frosi, Y. / Nakhle, J. / Tsomia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. ...Lama, D. / Liberator, A. / Frosi, Y. / Nakhle, J. / Tsomia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. / Ciesielski, F. / Uhring, M. | ||||||
Citation | Journal: Chem Sci / Year: 2019 Title: Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein. Authors: Lama, D. / Liberatore, A.M. / Frosi, Y. / Nakhle, J. / Tsomaia, N. / Bashir, T. / Lane, D.P. / Brown, C.J. / Verma, C.S. / Auvin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zk9.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zk9.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zk9 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zk9 | HTTPS FTP |
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-Related structure data
Related structure data | 5zjyC 5zjzC 5zk5C 5zk7C 5zmlC 4tpwS 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 22290.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / References: UniProt: P06730 |
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#2: Protein/peptide | Mass: 1684.165 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The acetylation (ACE) and amidation (NH2) are included in the SEQRES. Source: (synth.) Homo sapiens (human) |
-Non-polymers , 4 types, 170 molecules
#3: Chemical | ChemComp-MGP / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | AUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS BASED ON THE EIF4E INTERACTION ...AUTHORS STATE THAT THE CHAIN B IS A HYBRID SEQUENCE WHICH IS BASED ON THE EIF4E INTERACTIO |
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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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12.5% pEG1000 w/v, 12.5% PEG3350 w/v, 12.5% MPD w/v, 0.1M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.983994 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983994 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 22709 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rsym value: 0.048 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.76→1.86 Å / Mean I/σ(I) obs: 2.18 / Num. measured obs: 11964 / Num. unique obs: 3574 / Rsym value: 0.441 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TPW Resolution: 1.76→45.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.399 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.414 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→45.65 Å
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