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- PDB-6fhh: 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: 6fhh | |||||||||
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Title | Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated. | |||||||||
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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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 483.3 KB | Display | ![]() |
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PDB format | ![]() | 378.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 534.9 KB | Display | ![]() |
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Full document | ![]() | 560.4 KB | Display | |
Data in XML | ![]() | 73.4 KB | Display | |
Data in CIF | ![]() | 103.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fhiC ![]() 5m3hS S: Starting model for refinement C: citing same article ( |
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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 plus TEV protease site Source: (gene. exp.) ![]() Gene: PA / Production host: ![]() |
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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.) ![]() Gene: PB1 / Production host: ![]() |
#3: Protein | Mass: 91027.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PB2 / Production host: ![]() |
-RNA chain , 2 types, 2 molecules RV
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vRNA promoter 3' end / Source: (synth.) ![]() ![]() |
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#5: RNA chain | Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vRNA promoter 5' end / Source: (synth.) ![]() ![]() |
-Protein/peptide , 1 types, 2 molecules XY
#6: Protein/peptide | Mass: 2628.546 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Mimic of Pol II CTD with thiophospho-serine at position 5 Source: (synth.) ![]() |
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-Non-polymers , 3 types, 153 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-PO4 / #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop 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 thiophospho-serine-5 22-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 thiophospho-serine-5 22-mer Pol II CTD peptide mimic in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding. PH range: 5 |
-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: 2.7→50 Å / Num. obs: 92066 / % possible obs: 98.6 % / Redundancy: 2.92 % / CC1/2: 0.996 / Rsym value: 0.049 / Net I/σ(I): 14.34 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 2.69 % / Mean I/σ(I) obs: 1.87 / CC1/2: 0.761 / Rsym value: 0.5 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5m3h Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.635 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.685 / ESU R Free: 0.327 / 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: 90.198 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→50 Å
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Refine LS restraints |
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