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Yorodumi- PDB-7f07: Autonomous VH domain that interacts with eIF4E at the Capped mRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f07 | ||||||
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Title | Autonomous VH domain that interacts with eIF4E at the Capped mRNA Binding site. | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Inhibitor complex / Cap-Dependent Translation / VH domain | ||||||
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 / RNA 7-methylguanosine cap binding / 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 / 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 / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic stress granule / cytoplasmic ribonucleoprotein 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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Brown, C.J. / Frosi, Y. / Ng, S. / Lin, Y.C. | ||||||
Citation | Journal: Rsc Chem Biol / Year: 2022 Title: Development of a novel peptide aptamer that interacts with the eIF4E capped-mRNA binding site using peptide epitope linker evolution (PELE). Authors: Frosi, Y. / Ng, S. / Lin, Y.C. / Jiang, S. / Ramlan, S.R. / Lama, D. / Verma, C.S. / Asial, I. / 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 | 7f07.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f07.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 7f07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/7f07 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/7f07 | HTTPS FTP |
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-Related structure data
Related structure data | 7ezwC 4beaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli (E. coli) / References: UniProt: P06730 |
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#2: Protein | Mass: 19110.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Optimized autonomous VH Domain with a yeast display selected loop that interacts with target protein (eIF4E). Vh domain developed from 4D5 VH domain. Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS.HCl pH 8.5 25% (v/v) PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40.996 Å / Num. obs: 19226 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1 / Num. unique obs: 2734 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BEA Resolution: 2.25→40.943 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.212 / SU B: 8.758 / SU ML: 0.204 / Average fsc free: 0.8505 / Average fsc work: 0.8641 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.228 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.131 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→40.943 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: 20
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