+Open data
-Basic information
Entry | Database: PDB / ID: 6sw8 | ||||||
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Title | Crystal structure of the NS1 (H7N1) RNA-binding domain | ||||||
Components | Non-structural protein 1 | ||||||
Keywords | VIRAL PROTEIN / INFLUENZA VIRUS / RNA-BINDING DOMAIN / RNA BINDING PROTEIN | ||||||
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 / virus-mediated perturbation of host defense response / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.933 Å | ||||||
Authors | Coste, F. / Wacquiez, A. / Marc, D. / Castaing, B. | ||||||
Citation | Journal: Viruses / Year: 2020 Title: Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1. Authors: Wacquiez, A. / Coste, F. / Kut, E. / Gaudon, V. / Trapp, S. / Castaing, B. / Marc, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sw8.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sw8.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 6sw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sw8_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 6sw8_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 6sw8_validation.xml.gz | 9 KB | Display | |
Data in CIF | 6sw8_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6sw8 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6sw8 | HTTPS FTP |
-Related structure data
Related structure data | 6sx0C 6sx2C 6zlcC 5h5nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8817.149 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/turkey/Italy/977/1999(H7N1)) Strain: A/turkey/Italy/977/1999(H7N1) / Gene: ns1, NS, NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PST0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.14 Å3/Da / Density % sol: 70.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.12M (Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol) + 0.1M (Sodium HEPES, MOPS) + 37.5% (MPD, PEG 1000, PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98009 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→49.832 Å / Num. obs: 21170 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.93→1.97 Å / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 21170 / CC1/2: 0.704 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H5N Resolution: 1.933→49.832 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.85 Å2 / Biso mean: 54.5362 Å2 / Biso min: 29.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.933→49.832 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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