+Open data
-Basic information
Entry | Database: PDB / ID: 1bk6 | ||||||
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Title | KARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS | ||||||
Components |
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Keywords | COMPLEX (PROTEIN TRANSPORT/PEPTIDE) / PROTEIN TRANSPORT / NLS NUCLEAR IMPORT / ARMADILLO REPEAT CONTAINING PROTEIN / COMPLEX (PROTEIN TRANSPORT-PEPTIDE) / COMPLEX (PROTEIN TRANSPORT-PEPTIDE) complex | ||||||
Function / homology | Function and homology information proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / protein import into nucleus / disordered domain specific binding / nuclear envelope ...proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / protein import into nucleus / disordered domain specific binding / nuclear envelope / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.8 Å | ||||||
Authors | Conti, E. / Uy, M. / Leighton, L. / Blobel, G. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Authors: Conti, E. / Uy, M. / Leighton, L. / Blobel, G. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bk6.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bk6.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 1bk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bk6 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bk6 | HTTPS FTP |
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-Related structure data
-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: 46718.426 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: W303 / Cell line: BL21 / Cellular location: CYTOPLASMIC/NUCLEAR / Gene: SRP1 / Plasmid: PPROEX-HTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q02821 #2: Protein/peptide | Mass: 791.059 Da / Num. of mol.: 2 / Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) Source method: isolated from a genetically manipulated source Details: NLS PEPTIDE AT THE LARGER (FUNCTIONAL) BINDING SITE #3: Protein/peptide | Mass: 489.608 Da / Num. of mol.: 2 / Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) Source method: isolated from a genetically manipulated source Details: NLS PEPTIDE AT THE SMALLER BINDING SITE #4: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Dec 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.1 Å / Num. obs: 22717 / % possible obs: 86.9 % / Redundancy: 3.5 % / Rsym value: 0.064 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.188 / % possible all: 82.2 |
Reflection | *PLUS Num. measured all: 270860 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 82.2 % / Rmerge(I) obs: 0.188 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: UNLIGANDED KARYOPHERIN ALPHA Resolution: 2.8→29.1 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.85 Å / Total num. of bins used: 18
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.296 |