+Open data
-Basic information
Entry | Database: PDB / ID: 8tuq | ||||||
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Title | STL Polyomavirus LTA NLS bound to importin alpha 2 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / importin / karyopherin / nuclear / nls | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / DNA replication / postsynaptic density / hydrolase activity / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) STL polyomavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Donnelly, C.M. / Cross, E.M. / Forwood, J.K. / Alvisi, G. | ||||||
Funding support | 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin alpha-dependent nuclear localization signals. Authors: Cross, E.M. / Akbari, N. / Ghassabian, H. / Hoad, M. / Pavan, S. / Ariawan, D. / Donnelly, C.M. / Lavezzo, E. / Petersen, G.F. / Forwood, J.K. / Alvisi, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tuq.cif.gz | 222.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tuq.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tuq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/8tuq ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tuq | HTTPS FTP |
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-Related structure data
Related structure data | 8q8kC 8sudC 8turC 8tusC 8tutC 8tuuC 8tuvC 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: 55268.473 Da / Num. of mol.: 1 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: 2362.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) STL polyomavirus / References: UniProt: L7REU2 |
#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: 3.07 Å3/Da / Density % sol: 59.92 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.80 M sodium citrate, 0.1 M HEPES pH 6.5, 0.01 M DTT |
-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: Sep 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.21 Å / Num. obs: 47684 / % possible obs: 98.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 31.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.06 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3523 / CC1/2: 0.84 / Rpim(I) all: 0.31 / Rrim(I) all: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.21 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1007 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.21 Å
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Refine LS restraints |
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LS refinement shell |
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