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- PDB-5yf8: Crystals structure of Classical swine fever virus NS5B (residues ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yf8 | |||||||||
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Title | Crystals structure of Classical swine fever virus NS5B (residues 1-672, Y471A-E472A mutant) | |||||||||
![]() | RdRp catalytic | |||||||||
![]() | TRANSFERASE | |||||||||
Function / homology | ![]() serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing ...serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / proteolysis / RNA binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, W. / Gong, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase. Authors: Liu, W. / Shi, X. / Gong, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yf5C ![]() 5yf6C ![]() 5yf7C ![]() 6ae4C ![]() 6ae5C ![]() 6ae6C ![]() 6ae7C ![]() 2cjqS 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: 78006.289 Da / Num. of mol.: 1 / Mutation: Y471A, E472A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ACT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.93 % / Mosaicity: 1.293 ° |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 6 / Details: SOKALAN CP42 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.396→60 Å / Num. obs: 18873 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 67.37 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.059 / Rrim(I) all: 0.142 / Χ2: 0.995 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CJQ Resolution: 3.396→49.906 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.38 Å2 / Biso mean: 71.2286 Å2 / Biso min: 38.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.396→49.906 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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