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Yorodumi- PDB-5efa: Structure of Influenza B Lee PB2 cap-binding domain bound to m7GTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5efa | ||||||
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Title | Structure of Influenza B Lee PB2 cap-binding domain bound to m7GTP | ||||||
Components | Polymerase basic protein 2 | ||||||
Keywords | PROTEIN BINDING / cap-binding domain | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza B virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Ma, X. / Shia, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit. Authors: Xie, L. / Wartchow, C. / Shia, S. / Uehara, K. / Steffek, M. / Warne, R. / Sutton, J. / Muiru, G.T. / Leonard, V.H. / Bussiere, D.E. / Ma, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5efa.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5efa.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 5efa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/5efa ftp://data.pdbj.org/pub/pdb/validation_reports/ef/5efa | HTTPS FTP |
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-Related 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: 20441.531 Da / Num. of mol.: 1 / Fragment: cap-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Strain: B/Lee/1940 / Gene: PB2 / Plasmid: pTrcHis2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QLL6 |
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#2: Chemical | ChemComp-MGT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 42% PEG400, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å | ||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→87.79 Å / Num. obs: 13441 / % possible obs: 98.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Net I/σ(I): 11.3 / Num. measured all: 87469 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 1.9→36.658 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.72 Å2 / Biso mean: 28.958 Å2 / Biso min: 6.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→36.658 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: 5
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Refinement TLS params. | Method: refined / Origin x: 31.2689 Å / Origin y: 40.0063 Å / Origin z: 33.9703 Å
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Refinement TLS group |
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