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- PDB-5v5p: Structure of NLS2R of influenza A virus nucleoprotein bound to im... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v5p | ||||||
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Title | Structure of NLS2R of influenza A virus nucleoprotein bound to importin alpha | ||||||
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![]() | VIRAL PROTEIN / Nuclear Import / NLS | ||||||
Function / homology | ![]() 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 / helical viral capsid / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...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 / helical viral capsid / NLS-bearing protein import into nucleus / cytoplasmic stress granule / viral penetration into host nucleus / protein import into nucleus / host cell / viral nucleocapsid / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / host cell nucleus / structural molecule activity / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Synergy of two low-affinity NLSs determines the high avidity of influenza A virus nucleoprotein NP for human importin alpha isoforms. Authors: Wu, W. / Sankhala, R.S. / Florio, T.J. / Zhou, L. / Nguyen, N.L.T. / Lokareddy, R.K. / Cingolani, G. / Pante, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.7 KB | Display | ![]() |
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PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v5oC ![]() 5huyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57856.574 Da / Num. of mol.: 1 / Fragment: residues 2-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 2395.668 Da / Num. of mol.: 2 / Fragment: residues 10-28 / Source method: obtained synthetically / Details: Peptide was synthesized commercially Source: (synth.) ![]() References: UniProt: Q45VS8 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.11 % / Description: Rectangular blocks |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.6 M sodium citrate, 100 mM Hepes, and 10 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→15 Å / Num. obs: 42795 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rpim(I) all: 0.039 / Rsym value: 0.084 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.1 / Rpim(I) all: 0.32 / Rsym value: 0.69 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HUY Resolution: 2.15→14.986 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.69 / 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: 2.15→14.986 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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