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- PDB-5yvi: Crystal structure of Karyopherin beta2 in complex with FUS(456-526) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yvi | ||||||
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Title | Crystal structure of Karyopherin beta2 in complex with FUS(456-526) | ||||||
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![]() | PROTEIN TRANSPORT/RNA BINDING PROTEIN / Importin family / PROTEIN TRANSPORT / PROTEIN TRANSPORT-RNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular non-membrane-bounded organelle / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular non-membrane-bounded organelle / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / small GTPase binding / cilium / protein import into nucleus / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshizawa, T. / Fung, H.Y.J. / Chook, Y.M. | ||||||
![]() | ![]() Title: Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Authors: Yoshizawa, T. / Ali, R. / Jiou, J. / Fung, H.Y.J. / Burke, K.A. / Kim, S.J. / Lin, Y. / Peeples, W.B. / Saltzberg, D. / Soniat, M. / Baumhardt, J.M. / Oldenbourg, R. / Sali, A. / Fawzi, N.L. ...Authors: Yoshizawa, T. / Ali, R. / Jiou, J. / Fung, H.Y.J. / Burke, K.A. / Kim, S.J. / Lin, Y. / Peeples, W.B. / Saltzberg, D. / Soniat, M. / Baumhardt, J.M. / Oldenbourg, R. / Sali, A. / Fawzi, N.L. / Rosen, M.K. / Chook, Y.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349 KB | Display | ![]() |
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PDB format | ![]() | 284.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 451.4 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yvgC ![]() 5yvhC ![]() 4fddS 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: 98325.352 Da / Num. of mol.: 1 / Fragment: TRUNCATED RESIDUES 345-375 REPLACED WITH GGSGGSG Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 7561.034 Da / Num. of mol.: 1 / Fragment: C-terminal domain 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: 3.25 Å3/Da / Density % sol: 62.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8M Succinic acid |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→50 Å / Num. obs: 36917 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.049 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.73→2.78 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1669 / CC1/2: 0.597 / Rpim(I) all: 0.585 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FDD Resolution: 2.9→44.904 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→44.904 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.4202 Å / Origin y: 40.2364 Å / Origin z: 30.6658 Å
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Refinement TLS group |
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