+Open data
-Basic information
Entry | Database: PDB / ID: 5umz | |||||||||
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Title | Structure of TNRC6A NLS in complex with importin-alpha | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / mRNA decay / miRNA ARM repeat / nuclear transport | |||||||||
Function / homology | Function and homology information Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / maintenance of protein location in cell / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / miRNA-mediated gene silencing by inhibition of translation / NLS-dependent protein nuclear import complex / regulatory ncRNA-mediated gene silencing ...Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / maintenance of protein location in cell / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / miRNA-mediated gene silencing by inhibition of translation / NLS-dependent protein nuclear import complex / regulatory ncRNA-mediated gene silencing / postsynapse to nucleus signaling pathway / host cell / RISC complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cellular response to starvation / P-body / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / molecular adaptor activity / intracellular membrane-bounded organelle / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Chaston, J. / Stewart, A.G. / Christie, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Structural characterisation of TNRC6A nuclear localisation signal in complex with importin-alpha. Authors: Chaston, J.J. / Stewart, A.G. / Christie, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5umz.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5umz.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 5umz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/5umz ftp://data.pdbj.org/pub/pdb/validation_reports/um/5umz | HTTPS FTP |
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-Related structure data
Related structure data | 1pjnS 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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Details | As per the authors the biological assembly is a dimer, the second peptide bound is an artifact of the purification/crystallisation process |
-Components
#1: Protein | Mass: 55121.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-528 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 | ||||
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#2: Protein/peptide | Mass: 1502.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UHK8*PLUS #3: Chemical | ChemComp-GOL / #4: 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: 3.03 Å3/Da / Density % sol: 59.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, Hepes 7.0, 10mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2016 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→59.28 Å / Num. obs: 56250 / % possible obs: 100 % / Redundancy: 6.9 % / Rpim(I) all: 0.032 / Net I/σ(I): 19.8 |
Reflection shell | Rpim(I) all: 0.377 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PJN Resolution: 1.9→44.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 18.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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