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- PDB-6fhi: Crystal structure of bat influenza A/H17N10 polymerase with viral... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fhi | ||||||
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Title | Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 19-mer serine 5 phosphorylated Pol II CTD peptide with a truncated linker. | ||||||
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![]() | VIRAL PROTEIN / Influenza virus / RNA-dependent RNA polymerase / modified Pol II CTD peptide | ||||||
Function / homology | ![]() cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukarska, M. / Cusack, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Towards New Anti-Influenza Therapeutics: Structure-Activity Relationships in the Interaction between Heterotrimeric Influenza Polymerase and Pol II C-terminal domain Authors: Claron, M. / Lukarska, M. / Uhrig, U. / Sehr, P. / Drncova, P. / Lewis, J.D. / Will, D.W. / Cusack, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 475.7 KB | Display | ![]() |
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PDB format | ![]() | 375.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.9 KB | Display | ![]() |
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Full document | ![]() | 539.6 KB | Display | |
Data in XML | ![]() | 70.7 KB | Display | |
Data in CIF | ![]() | 99.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fhhC ![]() 5m3hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 protease site Source: (gene. exp.) ![]() ![]() ![]() |
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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 protease site Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 91027.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 2 types, 2 molecules RV
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3' end of vRNA promoter / Source: (synth.) ![]() ![]() |
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#5: RNA chain | Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' end of vRNA promoter / Source: (synth.) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules X
#6: Protein/peptide | Mass: 2215.072 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Serine 5 phosphoylated CTD like peptide with truncated linker Source: (synth.) ![]() |
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-Non-polymers , 2 types, 14 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PO4.gif)
#7: Chemical | ChemComp-ZN / |
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#8: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the serine 5 phosphorylated 19-mer Pol II CTD ...Details: Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the serine 5 phosphorylated 19-mer Pol II CTD peptide mimic, with a truncated linker, in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 81064 / % possible obs: 96.1 % / Redundancy: 2.19 % / CC1/2: 0.986 / Rsym value: 0.102 / Net I/σ(I): 6.35 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 1.43 / CC1/2: 0.687 / Rsym value: 0.589 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5m3h Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 17.492 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R: 1.479 / ESU R Free: 0.38 / 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: 81.201 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50 Å
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Refine LS restraints |
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