+Open data
-Basic information
Entry | Database: PDB / ID: 8q8k | ||||||
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Title | KI Polyomavirus LTA NLS bound to importin alpha 2 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / 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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / DNA replication / postsynaptic density / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / glutamatergic synapse / host cell nucleus / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) KI polyomavirus Stockholm 60 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | 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 | 8q8k.cif.gz | 302.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q8k.ent.gz | 244.4 KB | Display | PDB format |
PDBx/mmJSON format | 8q8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/8q8k ftp://data.pdbj.org/pub/pdb/validation_reports/q8/8q8k | HTTPS FTP |
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-Related structure data
Related structure data | 8sudC 8tuqC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55268.473 Da / Num. of mol.: 2 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 #2: Protein/peptide | Mass: 2412.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) KI polyomavirus Stockholm 60 / References: UniProt: P0DOI6 |
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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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.2 M NaCl, 0.1 M Tris pH 8.0, 16 % PEG4000. Protein stock pre-treated with 5:1 molar ratio IMPa: ivermectin |
-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: Mar 11, 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: 2.7→19.88 Å / Num. obs: 34296 / % possible obs: 99.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 67.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4564 / CC1/2: 0.76 / Rpim(I) all: 0.43 / Rrim(I) all: 0.67 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.88 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8368 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: 82.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.88 Å
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Refine LS restraints |
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LS refinement shell |
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