+Open data
-Basic information
Entry | Database: PDB / ID: 3w3y | ||||||
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Title | Crystal structure of Kap121p bound to Nup53p | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/DNA BINDING PROTEIN / HEAT repeat / nuclear import / PROTEIN TRANSPORT-DNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear import signal receptor activity / nuclear localization sequence binding ...response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / nuclear import signal receptor activity / nuclear localization sequence binding / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / mRNA transport / mRNA export from nucleus / nuclear pore / phospholipid binding / protein import into nucleus / single-stranded DNA binding / nuclear envelope / nuclear membrane / cell cycle / cell division / positive regulation of DNA-templated transcription / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kobayashi, J. / Matsuura, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p. Authors: Kobayashi, J. / Matsuura, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w3y.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w3y.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/3w3y ftp://data.pdbj.org/pub/pdb/validation_reports/w3/3w3y | HTTPS FTP |
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-Related structure data
Related structure data | 3w3tSC 3w3uC 3w3vC 3w3wC 3w3xC 3w3zC 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: 119912.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337 |
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#2: Protein/peptide | Mass: 5501.270 Da / Num. of mol.: 1 / Fragment: UNP residues 401-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: NUP53, YMR153W, YM8520.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03790 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2011 |
Radiation | Monochromator: rotated-inclined double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30.99 Å / Num. all: 33972 / Num. obs: 32341 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.94 Å / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3W3T Resolution: 2.8→30.33 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.941 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.549 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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