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- PDB-7vpw: Crystal structure of Transportin-1 in complex with BAP1 PY-NLS (r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vpw | ||||||
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Title | Crystal structure of Transportin-1 in complex with BAP1 PY-NLS (residues 706-724) | ||||||
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![]() | PROTEIN TRANSPORT / Transportin-1 / BRCA1-associated protein 1 / BAP1 / nuclear import / PY-NLS / deubiquitinase / DUB | ||||||
Function / homology | ![]() Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / small GTPase binding / cilium / protein import into nucleus / ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / small GTPase binding / cilium / protein import into nucleus / ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity / RNA binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, T.J. / Hsu, S.T.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tumor suppressor BAP1 nuclear import is governed by transportin-1. Authors: Yang, T.J. / Li, T.N. / Huang, R.S. / Pan, M.Y. / Lin, S.Y. / Lin, S. / Wu, K.P. / Wang, L.H. / Hsu, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.8 KB | Display | ![]() |
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PDB format | ![]() | 139.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.7 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z5oS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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/peptide | Mass: 2457.929 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 98511.586 Da / Num. of mol.: 1 Fragment: UNP residues 8-344, UNP residues 376-898,UNP residues 376-898 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.49 M Sodium phosphate monobasic monohydrate, 0.91 M Sodium phosphate dibasic, pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.76→103.2 Å / Num. obs: 16059 / % possible obs: 99.6 % / Redundancy: 6.88 % / Biso Wilson estimate: 133.33 Å2 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.09 / Rsym value: 0.23 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3.76→3.88 Å / Num. unique obs: 795 / CC1/2: 0.905 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2z5o Resolution: 3.76→63.86 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 222.16 Å2 / Biso mean: 145.5931 Å2 / Biso min: 81.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.76→63.86 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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