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- PDB-7z43: Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z43 | ||||||
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Title | Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 1B and 2B | ||||||
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![]() | RNA BINDING PROTEIN / Influenza RNA-dependent RNA polymerase / transcription / cap-snatching / Pol II CTD | ||||||
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 / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...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 / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. / Drncova, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD. Authors: Krischuns, T. / Isel, C. / Drncova, P. / Lukarska, M. / Pflug, A. / Paisant, S. / Navratil, V. / Cusack, S. / Naffakh, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 498.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 845.8 KB | Display | ![]() |
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Full document | ![]() | 859.6 KB | Display | |
Data in XML | ![]() | 71.8 KB | Display | |
Data in CIF | ![]() | 99.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z42C ![]() 7z4oC ![]() 5msgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 AAABBBCCC
#1: Protein | Mass: 85822.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal His-tag C-terminal linker and TEV site / Source: (gene. exp.) ![]() ![]() References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 86207.016 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: 90844.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal STREP-tag and TEV protease site Source: (gene. exp.) ![]() ![]() |
-RNA chain , 3 types, 3 molecules RRRVVVMaM
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vRNA template / Source: (synth.) ![]() |
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#5: RNA chain | Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5' vRNA hook / Source: (synth.) ![]() |
#6: RNA chain | Mass: 4110.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Capped RNA primer / Source: (synth.) ![]() |
-Protein/peptide , 1 types, 2 molecules XXXYYY
#7: Protein/peptide | Mass: 3216.893 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Four repeats of Pol II CTD heptad with pSer5 / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 3 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/IC5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IC5.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-PO4 / |
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#9: Chemical | ChemComp-IC5 / [( |
#10: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.33 Å3/Da / Density % sol: 76.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 200 mM di-ammonium phosphate, and 100 mM sodium acetate at pH 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→76.972 Å / Num. obs: 77848 / % possible obs: 73.1 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.149 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.12→3.32 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3951 / CC1/2: 0.536 / Rrim(I) all: 1.49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MSG Resolution: 3.123→76.972 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.879 / SU B: 25.401 / SU ML: 0.388 / Cross valid method: FREE R-VALUE / ESU R: 17.94 / ESU R Free: 0.48 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.854 Å2
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Refinement step | Cycle: LAST / Resolution: 3.123→76.972 Å
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Refine LS restraints |
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LS refinement shell |
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