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Yorodumi- PDB-1pjn: Mouse Importin alpha-bipartite NLS N1N2 from Xenopus laevis phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pjn | ||||||
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Title | Mouse Importin alpha-bipartite NLS N1N2 from Xenopus laevis phosphoprotein Complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / IMPORTIN ALPHA/KARYOPHERIN ALPHA / NUCLEAR LOCALIZATION SEQUENCE (NLS) RECOGNITION / BIPARTITE NLS / Xenopus laevis N1N2 phosphoprotein | ||||||
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 / positive regulation of viral life cycle / importin-alpha family protein binding / 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 / host cell ...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 / importin-alpha family protein binding / 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 / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha Authors: Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha Authors: Fontes, M.R.M. / Teh, T. / Kobe, B. #2: Journal: J.Biol.Chem. / Year: 2001 Title: Biophysical Characterization of Interactions Involving Impostin-alpha during Nuclear Import Authors: Catimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Jans, D. / Howlett, G.J. / Nice, E.C. / Kobe, B. #3: Journal: Nat.Struct.Biol. / Year: 1999 Title: Autoinhibition by an internal nuclear localization signal reveled by the crystal structure of mammalian importin alpha Authors: Kobe, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pjn.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pjn.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pjn ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pjn | HTTPS FTP |
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-Related structure data
Related structure data | 1pjmC 1ialS 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/peptide | Mass: 2481.932 Da / Num. of mol.: 1 Fragment: NLS (nuclear localization signal) bipartite peptide Mutation: Q555G / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN Xenopus laevis N1N2 phosphoprotein References: UniProt: P52293, UniProt: P06180*PLUS |
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#2: Protein | Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P06180, UniProt: P52293*PLUS |
#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: 3.42 Å3/Da / Density % sol: 63.99 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2000 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. all: 25538 / Num. obs: 25538 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.8 / % possible all: 94.6 |
Reflection | *PLUS Num. measured all: 211968 |
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY: 1ial Resolution: 2.5→29.64 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.0074 Å2 / ksol: 0.348618 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.302 |