+Open data
-Basic information
Entry | Database: PDB / ID: 7xtp | ||||||
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Title | eIF4E in Complex with a Disulphide-Free Autonomous VH Domain | ||||||
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 / 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: 1.828 Å | ||||||
Authors | Brown, C.J. / Frosi, Y. / Jiang, S. / Lin, Y.C. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Engineering an autonomous VH domain to modulate intracellular pathways and to interrogate the eIF4F complex. Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. ...Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. / Thean, D. / Lane, D.P. / 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 | 7xtp.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xtp.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtp ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtp | HTTPS FTP |
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-Related structure data
Related structure data | 7d8bC 7d6yS 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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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) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06730 #2: Protein | Mass: 16504.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Engineered Autonomous VH domain with Intra-disulphide Bond. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.05 Å3/Da / Density % sol: 39.89 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium HEPES pH7.5, 25% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.828→46.332 Å / Num. obs: 59269 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 18.7 Å2 / Rrim(I) all: 0.147 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.828→1.89 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3593 / Rrim(I) all: 1.691 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D6Y Resolution: 1.828→46.332 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.216 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.166 / ESU R Free: 0.149 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: 22.465 Å2
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Refinement step | Cycle: LAST / Resolution: 1.828→46.332 Å
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Refine LS restraints |
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LS refinement shell |
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