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Yorodumi- PDB-3d6r: Structure of an avian influenza A virus NS1 protein effector domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d6r | ||||||
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Title | Structure of an avian influenza A virus NS1 protein effector domain | ||||||
Components | Non-structural protein 1 | ||||||
Keywords | VIRAL PROTEIN / Influenza / NS1 / effector domain / Alternative splicing / Cytoplasm / Host-virus interaction / Interferon antiviral system evasion / Nucleus / RNA-binding / Suppressor of RNA silencing | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.997 Å | ||||||
Authors | Hale, B.G. / Barclay, W.S. / Randall, R.E. / Russell, R.J. | ||||||
Citation | Journal: Virology / Year: 2008 Title: Structure of an avian influenza A virus NS1 protein effector domain. Authors: Hale, B.G. / Barclay, W.S. / Randall, R.E. / Russell, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d6r.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d6r.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d6r_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 3d6r_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 3d6r_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3d6r_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/3d6r ftp://data.pdbj.org/pub/pdb/validation_reports/d6/3d6r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17754.348 Da / Num. of mol.: 2 / Fragment: effector domain (UNP residues 73-230) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Alberta/60/1976 H12N5 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P69270 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8K, hepes, Na thiocyanate, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 30438 / Num. obs: 26147 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.62 Å2 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→19.97 Å / FOM work R set: 0.858 / σ(F): 1.9 / 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 / Bsol: 58.602 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 9.73 Å2 / Biso mean: 26.88 Å2 / Biso min: 74.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.997→19.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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