+Open data
-Basic information
Entry | Database: PDB / ID: 4wsb | ||||||
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Title | Bat Influenza A polymerase with bound vRNA promoter | ||||||
Components |
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Keywords | transferase/rna / transferase-rna complex | ||||||
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 unidentified influenza virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Cusack, S. / Pflug, A. / Guilligay, D. / Reich, S. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Authors: Reich, S. / Guilligay, D. / Pflug, A. / Malet, H. / Berger, I. / Crepin, T. / Hart, D. / Lunardi, T. / Nanao, M. / Ruigrok, R.W. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wsb.cif.gz | 475.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wsb.ent.gz | 373.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/4wsb ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4wsb | HTTPS FTP |
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-Related structure data
Related structure data | 4wrtC 4wsaSC 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 extension: his-tag C-terminal extension: linker and TEV site Source: (gene. exp.) Influenza A virus Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) Gene: PA / Plasmid: pKL-PBac / Cell line (production host): High Five / 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 extension: linker C-terminal extension: linker and TEV site Source: (gene. exp.) Influenza A virus Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) Gene: PB1 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM91, RNA-directed RNA polymerase |
#3: Protein | Mass: 89012.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal extension: linker C-terminal extension: Strep-tag and TEV site Source: (gene. exp.) Influenza A virus Strain: A/little yellow-shouldered bat/Guatemala/060/2010(H17N10) Gene: PB2 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H6QM90 |
-Influenza A polymerase vRNA promoter ... , 2 types, 2 molecules RV
#4: RNA chain | Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus |
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#5: RNA chain | Mass: 5248.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus |
-Non-polymers , 3 types, 50 molecules
#6: Chemical | ChemComp-ZN / | ||
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#7: Chemical | ChemComp-PO4 / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.73 % |
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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 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: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 99462 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.439 / Mean I/σ(I) obs: 1.14 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSA Resolution: 2.65→19.996 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.65→19.996 Å
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Refine LS restraints |
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LS refinement shell |
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