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- PDB-8ech: Tick-borne encephalitis virus capsid protein NLS bound to host im... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ech | ||||||
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Title | Tick-borne encephalitis virus capsid protein NLS bound to host importin alpha 2 | ||||||
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![]() | VIRAL PROTEIN / bipartite / nuclear import / capsid | ||||||
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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus ...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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / viral capsid / DNA-binding transcription factor binding / membrane => GO:0016020 / postsynaptic density / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / glutamatergic synapse / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roby, J.A. / Forwood, J.K. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure and biological functions of tick-borne encephalitis virus capsid protein Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / ...Authors: Selinger, M. / Novotny, R. / Sys, J. / Roby, J.A. / Tykalova, H. / Ranjani, G.S. / Vancova, M. / Jaklova, K. / Kaufman, F. / Bloom, M.E. / Zdrahal, Z. / Grubhoffer, L. / Forwood, J.K. / Hrabal, R. / Rumlova, M. / Sterba, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.6 KB | Display | ![]() |
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PDB format | ![]() | 138.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 443.3 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bw0S 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: 2578.204 Da / Num. of mol.: 1 / Fragment: residues 76-96 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: M1LJY4 |
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#2: Protein | Mass: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P52293 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.7 M sodium citrate, 0.1 M HEPES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.52 Å / Num. obs: 44694 / % possible obs: 100 % / Redundancy: 12 % / Rpim(I) all: 0.039 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.05→2.11 Å / Num. unique obs: 3429 / Rpim(I) all: 0.33 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6bw0 Resolution: 2.05→29.52 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→29.52 Å
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Refine LS restraints |
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LS refinement shell |
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