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Yorodumi- PDB-2vy8: The 627-domain from influenza A virus polymerase PB2 subunit with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vy8 | ||||||
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Title | The 627-domain from influenza A virus polymerase PB2 subunit with Glu- 627 | ||||||
Components | POLYMERASE BASIC PROTEIN 2 | ||||||
Keywords | TRANSCRIPTION / VIRAL PROTEIN / MRNA CAPPING / MITOCHONDRION / MRNA PROCESSING | ||||||
Function / homology | Function and homology information cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Tarendeau, F. / Crepin, T. / Guilligay, D. / Ruigrok, R. / Cusack, S. / Hart, D. | ||||||
Citation | Journal: Plos Pathog. / Year: 2008 Title: Host Determinant Residue Lysine 627 Lies on the Surface of a Discrete, Folded Domain of Influenza Virus Polymerase Pb2 Subunit Authors: Tarendeau, F. / Crepin, T. / Guilligay, D. / Ruigrok, R. / Cusack, S. / Hart, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vy8.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vy8.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 2vy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vy8_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 2vy8_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 2vy8_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2vy8_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vy8 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vy8 | HTTPS FTP |
-Related structure data
Related structure data | 2vy6C 2vy7SC 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 | Mass: 17721.197 Da / Num. of mol.: 1 / Fragment: 627-DOMAIN, RESIDUES 538-693 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/1975(H3N2) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI RIL / References: UniProt: P31345 | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | K627E MUTATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Details: 1 MICROLITRE OF 2.4 MG/ML PROTEIN SOLUTION IN 10 MM TRIS-HCL PH 7.0 AND 200 MM NACL WITH 1 MICROLITRE OF 100 MM CITRIC ACID PH 4.0-7.0 AND 1.4-1.6 M AMMONIUM SULFATE SOLUTION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→30 Å / Num. obs: 42201 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.07 |
Reflection shell | Resolution: 1.15→1.2 Å / Redundancy: 1.39 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 627-DOMAIN WITH K627 FROM PDB ENTRY 2VY7 Resolution: 1.2→29.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.82 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→29.21 Å
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Refine LS restraints |
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