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Yorodumi- PDB-5nvm: Crystal structure of the human 4EHP-GIGYF2 complex lacking the au... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nvm | ||||||
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Title | Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences | ||||||
Components |
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Keywords | TRANSLATION / translational regulation / cap-binding protein / 4EHP-binding protein / GRB10-interacting GYF protein 2 | ||||||
Function / homology | Function and homology information musculoskeletal movement / post-transcriptional gene silencing / spinal cord motor neuron differentiation / proximal dendrite / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding ...musculoskeletal movement / post-transcriptional gene silencing / spinal cord motor neuron differentiation / proximal dendrite / RNA cap binding / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / mRNA cap binding / miRNA-mediated gene silencing by inhibition of translation / RNA 7-methylguanosine cap binding / feeding behavior / proline-rich region binding / negative regulation of type I interferon-mediated signaling pathway / mRNA destabilization / neuromuscular process controlling balance / rescue of stalled ribosome / homeostasis of number of cells within a tissue / negative regulation of translational initiation / mitotic G1 DNA damage checkpoint signaling / translation initiation factor activity / adult locomotory behavior / post-embryonic development / insulin-like growth factor receptor signaling pathway / P-body / multicellular organism growth / ISG15 antiviral mechanism / cytoplasmic stress granule / perikaryon / vesicle / negative regulation of translation / molecular adaptor activity / endosome / cadherin binding / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / protein-containing complex / RNA binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Peter, D. / Valkov, E. | ||||||
Citation | Journal: Genes Dev. / Year: 2017 Title: GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression. Authors: Peter, D. / Weber, R. / Sandmeir, F. / Wohlbold, L. / Helms, S. / Bawankar, P. / Valkov, E. / Igreja, C. / Izaurralde, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nvm.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nvm.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 5nvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/5nvm ftp://data.pdbj.org/pub/pdb/validation_reports/nv/5nvm | HTTPS FTP |
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-Related structure data
Related structure data | 5nvkC 5nvlSC 5nvnC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21979.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first six residues of the coordinate sequence belong to the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E2, EIF4EL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: O60573 #2: Protein/peptide | Mass: 5018.892 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GIGYF2, KIAA0642, PERQ2, TNRC15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6Y7W6 #3: Chemical | ChemComp-PO4 / #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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.6 0.6 M diammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.613 Å / Num. obs: 38577 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rsym value: 0.066 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.09 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NVL Resolution: 2→44.613 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.613 Å
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Refine LS restraints |
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LS refinement shell |
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