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Yorodumi- PDB-6evk: Crystal structure of bat influenza A/H17N10 polymerase with viral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6evk | ||||||
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Title | Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP | ||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza virus / RNA-dependent RNA polymerase / cap analogue | ||||||
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 / viral transcription / host cell mitochondrion / virion component / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / virion component / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Pflug, A. / Cusack, S. | ||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors. Authors: Pflug, A. / Gaudon, S. / Resa-Infante, P. / Lethier, M. / Reich, S. / Schulze, W.M. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6evk.cif.gz | 477.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6evk.ent.gz | 374 KB | Display | PDB format |
PDBx/mmJSON format | 6evk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6evk ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6evk | HTTPS FTP |
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-Related structure data
Related structure data | 6euvC 6euwC 6euxC 6euyC 6evjC 4wsbS 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 85490.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag C-terminal linker and TEV cleavage site Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM92 |
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#2: Protein | Mass: 87936.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal linker and TEV cleavage site Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase |
#3: Protein | Mass: 91027.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal linker, STREP-tag and TEV cleavage site Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)) Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90 |
-RNA chain , 2 types, 2 molecules RV
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Viral RNA promoter 3 primed end / Source: (synth.) Influenza A virus |
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#5: RNA chain | Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Influenza viral RNA promoter 5 primed end / Source: (synth.) Influenza A virus |
-Non-polymers , 4 types, 52 molecules
#6: Chemical | ChemComp-ZN / | ||||
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#7: Chemical | ChemComp-PO4 / #8: Chemical | ChemComp-MGP / | #9: 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: 3.19 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which ...Details: Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which was an equimolar mixture of nucleotides 1-16 from the 5 prime end and nucleotides 1-18 or 3-18 from the 3 prime end. Protein-RNA with the addition of 5 mM m7GTP was mixed with mother liquor containing 0.7-1.5 M sodium-potassium phosphate at pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 76144 / % possible obs: 99.6 % / Redundancy: 4.63 % / CC1/2: 0.998 / Rrim(I) all: 0.115 / Rsym value: 0.102 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 4.65 % / Mean I/σ(I) obs: 1.08 / CC1/2: 0.597 / Rrim(I) all: 1.38 / Rsym value: 1.22 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSB Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 24.407 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.697 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→50 Å
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Refine LS restraints |
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