+Open data
-Basic information
Entry | Database: PDB / ID: 8tka | ||||||
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Title | Structure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant | ||||||
Components | Protein sigma-NS | ||||||
Keywords | RNA BINDING PROTEIN / RNA-binding protein / RNA chaperone | ||||||
Function / homology | Reovirus non-structural protein sigma NS / Sigma NS protein / host cell cytoplasm / single-stranded RNA binding / RNA-dependent RNA polymerase activity / Protein sigma-NS Function and homology information | ||||||
Biological species | Mammalian orthoreovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Prasad, B.V.V. / Zhao, B. / Hu, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of orthoreovirus RNA chaperone sigma NS, a component of viral replication factories. Authors: Zhao, B. / Hu, L. / Kaundal, S. / Neetu, N. / Lee, C.H. / Somoulay, X. / Sankaran, B. / Taylor, G.M. / Dermody, T.S. / Venkataram Prasad, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tka.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tka.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 8tka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tka_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 8tka_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 8tka_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 8tka_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/8tka ftp://data.pdbj.org/pub/pdb/validation_reports/tk/8tka | HTTPS FTP |
-Related structure data
Related structure data | 8tl1C 8tl8C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42136.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammalian orthoreovirus 1 / Gene: S3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03526 Has ligand of interest | Y | |
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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: 3.24 Å3/Da / Density % sol: 62.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2% colic acid derivative, 0.1M buffer system 3 and 30% precipitant mix 3 (molecular dimension) |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→118.74 Å / Num. obs: 41323 / % possible obs: 99.64 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.069 / Num. unique obs: 29506 / Rpim(I) all: 0.023 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→118.74 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.881 / SU B: 24.392 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.303 Å2
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Refinement step | Cycle: 1 / Resolution: 3→118.74 Å
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