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Open data
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Basic information
Entry | Database: PDB / ID: 3w3x | ||||||
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Title | Crystal structure of Kap121p bound to Pho4p | ||||||
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![]() | PROTEIN TRANSPORT/TRANSCRIPTION / HEAT repeat / nuclear import / PROTEIN TRANSPORT-TRANSCRIPTION complex | ||||||
Function / homology | ![]() positive regulation of phosphate metabolic process / regulation of protein desumoylation / cellular response to phosphate starvation / nuclear import signal receptor activity / regulation of mitotic nuclear division / nuclear localization sequence binding / mRNA export from nucleus / protein import into nucleus / sequence-specific DNA binding / protein dimerization activity ...positive regulation of phosphate metabolic process / regulation of protein desumoylation / cellular response to phosphate starvation / nuclear import signal receptor activity / regulation of mitotic nuclear division / nuclear localization sequence binding / mRNA export from nucleus / protein import into nucleus / sequence-specific DNA binding / protein dimerization activity / chromatin remodeling / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kobayashi, J. / Matsuura, Y. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.5 KB | Display | ![]() |
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PDB format | ![]() | 161.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3w3tSC ![]() 3w3uC ![]() 3w3vC ![]() 3w3wC ![]() 3w3yC ![]() 3w3zC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 2938.281 Da / Num. of mol.: 1 / Fragment: UNP residues 140-166 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
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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: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29.97 Å / Num. all: 28698 / Num. obs: 28382 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→3.08 Å / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3W3T Resolution: 2.9→29.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 18.531 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / 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: 75.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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