+Open data
-Basic information
Entry | Database: PDB / ID: 6d7n | |||||||||
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Title | Crystal structure of the W357R/W399R Importin alpha mutant | |||||||||
Components | Peroxidase,Importin subunit alpha-1 | |||||||||
Keywords | TRANSPORT PROTEIN / IMPORTIN / NLS / BIPARTITE / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / lactoperoxidase activity / peroxidase / 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 ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / lactoperoxidase activity / peroxidase / 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 / hydrogen peroxide catabolic process / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / response to oxidative stress / postsynaptic density / glutamatergic synapse / heme binding / extracellular region / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Panicum virgatum (switchgrass) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Pedersen, L.C. / London, R.E. / Gabel, S.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Traffic / Year: 2018 Title: Variations in nuclear localization strategies among pol X family enzymes. Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d7n.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d7n.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 6d7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/6d7n ftp://data.pdbj.org/pub/pdb/validation_reports/d7/6d7n | HTTPS FTP |
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-Related structure data
Related structure data | 5w4eC 5w4fC 6d7mC 5e6qS 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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Unit cell |
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-Components
#1: Protein | Mass: 55272.535 Da / Num. of mol.: 1 / Mutation: W357R, W399R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass), (gene. exp.) Mus musculus (house mouse) Gene: PviPRX9, Kpna2, Rch1 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1S4NYF8, UniProt: P52293, peroxidase | ||
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#2: Chemical | ChemComp-EDO / #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: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0M triammonium citrate, 0.1M Bis-Tris-Propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 28, 2018 / Details: VariMaxHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 32563 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.064 / Rrim(I) all: 0.164 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1571 / CC1/2: 0.749 / Rpim(I) all: 0.395 / Rrim(I) all: 0.979 / Rsym value: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E6Q Resolution: 2.3→29.287 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 22.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.287 Å
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Refine LS restraints |
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LS refinement shell |
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