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Yorodumi- PDB-8tl8: Structure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tl8 | ||||||
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Title | Structure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant in complex with bile acid | ||||||
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 / GLYCOCHOLIC ACID / Protein sigma-NS Function and homology information | ||||||
Biological species | Orthoreovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Prasad, B.V.V. / Zhao, B. / Hu, L. / Neetu, N. | ||||||
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 | 8tl8.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tl8.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tl8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8tl8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8tl8_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 8tl8_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/8tl8 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/8tl8 | HTTPS FTP |
-Related structure data
Related structure data | 8tkaC 8tl1C 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: 41104.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orthoreovirus / Gene: S3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03526 #2: Chemical | ChemComp-GCH / 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: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.2% colic acid derivative mix, 0.1 M Buffer System 3 (pH 8.5), and 30% Precipitant Mix 3 (Molecular Dimensions) |
-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: May 5, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.1→76.38 Å / Num. obs: 12953 / % possible obs: 81.7 % / Redundancy: 1 % / Biso Wilson estimate: 62.51 Å2 / Rmerge(I) obs: 0.0311 / Rpim(I) all: 0.0311 / Rrim(I) all: 0.04398 / Net I/σ(I): 18.04 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→34.22 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.23 / 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: 3.2→34.22 Å
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Refine LS restraints |
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LS refinement shell |
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