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Yorodumi- PDB-5fml: Crystal structure of the endonuclease from the PA subunit of infl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fml | ||||||
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Title | Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide | ||||||
Components |
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Keywords | VIRAL PROTEIN / ENDONUCLEASE | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / RNA-dependent RNA polymerase activity ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | INFLUENZA B VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Guilligay, D. / Gaudon, S. / Cusack, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2016 Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains. Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fml.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fml.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fml_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 5fml_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 5fml_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 5fml_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fml ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fml | HTTPS FTP |
-Related structure data
Related structure data | 5epiC 5fmmC 5fmqC 5fmzC 4wrtS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein/peptide | Mass: 3318.807 Da / Num. of mol.: 1 / Fragment: NLS PEPTIDE RESIDUES 742-770 / Source method: obtained synthetically / Source: (synth.) INFLUENZA B VIRUS / References: UniProt: Q5V8X3 | ||||||||
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#2: Protein | Mass: 23333.469 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE DOMAIN RESIDUES 1-197 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA B VIRUS / Strain: B/MEMPHIS/13/2003/ / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: Q5V8Z9 | ||||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Nonpolymer details | GLYCEROL (GOL): CRYOPROTEC | Sequence details | ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.3 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M MES PH 6.5, 25% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 22279 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.72 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.68 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.84 / % possible all: 93 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4WRT Resolution: 1.7→40.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.671 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.895 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40.42 Å
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Refine LS restraints |
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