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- PDB-7z42: 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: 7z42 | ||||||
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Title | Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 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 | ![]() | 925.9 KB | Display | ![]() |
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PDB format | ![]() | 721.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 560.4 KB | Display | ![]() |
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Full document | ![]() | 607.2 KB | Display | |
Data in XML | ![]() | 139.8 KB | Display | |
Data in CIF | ![]() | 195.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z43C ![]() 7z4oC ![]() 5fmzS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 85822.781 Da / Num. of mol.: 2 / Mutation: K135A 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 #2: Protein | Mass: 86207.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal linker and TEV site / Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 90844.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal linker C-terminal STREP-tag and TEV site Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide / RNA chain / Non-polymers , 3 types, 212 molecules YGXIHV![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Protein/peptide | Mass: 3216.893 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Four repeat Pol II CTD peptide mimic with pSer5 / Source: (synth.) ![]() References: DNA-directed RNA polymerase, RNA-directed RNA polymerase #5: RNA chain | Mass: 4212.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5' vRNA hook / Source: (synth.) ![]() #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 ...Details: FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25422 Å / Relative weight: 1 |
Reflection | Resolution: 2.418→127.106 Å / Num. obs: 154519 / % possible obs: 61.4 % / Redundancy: 3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.136 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.42→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7573 / CC1/2: 0.63 / Rrim(I) all: 0.769 / % possible all: 64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FMZ Resolution: 2.418→127.106 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.223 / SU B: 9.426 / SU ML: 0.215 / Average fsc free: 0.8891 / Average fsc work: 0.9001 / Cross valid method: FREE R-VALUE / ESU R: 2.182 / ESU R Free: 0.367 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: 54.204 Å2
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Refinement step | Cycle: LAST / Resolution: 2.418→127.106 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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