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Yorodumi- PDB-1ee5: YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ee5 | ||||||
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Title | YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLASMIN NLS PEPTIDE | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Armadillo repeat | ||||||
Function / homology | Function and homology information sperm DNA decondensation / proteasome localization / histone chaperone activity / import into nucleus / importin-alpha family protein binding / 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 ...sperm DNA decondensation / proteasome localization / histone chaperone activity / import into nucleus / importin-alpha family protein binding / 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 / nucleosome binding / positive regulation of DNA replication / protein import into nucleus / disordered domain specific binding / nuclear envelope / histone binding / chromatin remodeling / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Conti, E. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha. Authors: Conti, E. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ee5.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ee5.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ee5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ee5_validation.pdf.gz | 370.5 KB | Display | wwPDB validaton report |
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Full document | 1ee5_full_validation.pdf.gz | 377.9 KB | Display | |
Data in XML | 1ee5_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1ee5_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1ee5 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1ee5 | HTTPS FTP |
-Related 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: 46927.578 Da / Num. of mol.: 1 / Fragment: ARMADILLLO-REPEAT DOMAIN / Mutation: Y397D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q02821 |
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#2: Protein/peptide | Mass: 2030.545 Da / Num. of mol.: 1 / Fragment: NLS (NUCLEAR LOCALIZATION SEQUENCE) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / References: UniProt: P05221 |
#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: 3.16 Å3/Da / Density % sol: 61.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: SYNCHROTRON / Site: CHESS / Beamline: A1 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 21907 / % possible obs: 90.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 2.4→30 Å / Rmerge(I) obs: 0.286 / % possible all: 80 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 21907 / Num. measured all: 105706 |
Reflection shell | *PLUS % possible obs: 80 % / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
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Refinement | Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber /
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.241 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |