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Yorodumi- PDB-4ye2: The 1.35 structure of a viral RNase L antagonist reveals basis fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ye2 | ||||||
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Title | The 1.35 structure of a viral RNase L antagonist reveals basis for the 2'-5'-oligoadenylate binding and enzyme activity. | ||||||
Components | Capping enzyme protein | ||||||
Keywords | VIRAL PROTEIN / innate immunity / RNase L / oligoadenylate / rotavirus / coronavirus / phosphodiesterase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / : / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / RNA binding Similarity search - Function | ||||||
Biological species | Rotavirus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.098 Å | ||||||
Authors | Hu, L. / Sankaran, B. / Prasad, B.V.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Virol. / Year: 2015 Title: Structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral RNase L antagonist. Authors: Ogden, K.M. / Hu, L. / Jha, B.K. / Sankaran, B. / Weiss, S.R. / Silverman, R.H. / Patton, J.T. / 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 | 4ye2.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ye2.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ye2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4ye2 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4ye2 | HTTPS FTP |
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-Related structure data
Related structure data | 4rptSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16766.479 Da / Num. of mol.: 2 / Fragment: UNP residues 694-835 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A / Strain: RRV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B3F2X4 #2: Chemical | ChemComp-A2P / | #3: Chemical | ChemComp-SO4 / | #4: 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: 3.89 Å3/Da / Density % sol: 68.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES sodium, 2% PEG400, 2.0M Ammonium sulfate PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976484 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 |
Reflection | Resolution: 3.098→35 Å / Num. all: 10134 / Num. obs: 10030 / % possible obs: 99.9 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RPT Resolution: 3.098→34.503 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.49 / 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: 3.098→34.503 Å
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Refine LS restraints |
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LS refinement shell |
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