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- PDB-8fk3: Adeno-Associated Virus Porcine Origin capsid protein basic region... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fk3 | ||||||
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Title | Adeno-Associated Virus Porcine Origin capsid protein basic regions in complex with Importin-alpha 2 | ||||||
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![]() | TRANSPORT PROTEIN / importin / alpha / adeno associated / complex / basic regions / transport / nucleus | ||||||
Function / homology | ![]() Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=1 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / structural molecule activity / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoad, M. / Forwood, J.K. / Roby, J.A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal. Authors: Hoad, M. / Cross, E.M. / Donnelly, C.M. / Sarker, S. / Roby, J.A. / Forwood, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.6 KB | Display | ![]() |
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PDB format | ![]() | 132.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.5 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oihS 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 | Mass: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4645.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.75M Na Citrate, 0.01M DTT, 0.1M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.96 Å / Num. obs: 21468 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 50.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 0.643 / Num. unique obs: 2616 / CC1/2: 0.639 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4oih Resolution: 2.6→19.96 Å / SU ML: 0.339 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3277 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 58.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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