+Open data
-Basic information
Entry | Database: PDB / ID: 7d6y | ||||||
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Title | eIF4E in Complex with a Disulphide-Free Autonomous VH Domain | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / VH domain / 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 / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.668 Å | ||||||
Authors | Brown, C.J. / Frosi, Y. / Jiang, S. / Lin, Y.C. | ||||||
Citation | Journal: To Be Published Title: Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways Authors: Frosi, Y. / Lin, Y.C. / Jiang, S. / Ramlan, S.R. / Hew, K. / Asial, I. / Engman, A.H. / Goh, M. / Thean, D. / Nordlund, P. / 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 | 7d6y.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6y.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 7d6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6y ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6y | HTTPS FTP |
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-Related structure data
Related structure data | 2v8wS 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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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 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P06730 |
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#2: Protein | Mass: 17154.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-MGO / [[( |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5 |
-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: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.668→44.229 Å / Num. obs: 41261 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 3.3 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.67→1.76 Å / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V8W Resolution: 1.668→44.226 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.24 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.097 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: 12.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.668→44.226 Å
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Refine LS restraints |
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LS refinement shell |
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