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Yorodumi- PDB-2vy6: Two domains from the C-terminal region of influenza A virus polym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vy6 | ||||||
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Title | Two domains from the C-terminal region of influenza A virus polymerase PB2 subunit | ||||||
Components | POLYMERASE BASIC PROTEIN 2 | ||||||
Keywords | TRANSCRIPTION / MRNA CAPPING / MITOCHONDRION / MRNA PROCESSING / VIRAL PROTEIN | ||||||
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / cap snatching / virion component / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription ...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 / cap snatching / virion component / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 2vy6.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vy6.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vy6_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 2vy6_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 2vy6_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2vy6_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vy6 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vy6 | HTTPS FTP |
-Related structure data
Related structure data | 2vy7SC 2vy8C 2jdqS 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
#1: Protein | Mass: 24329.936 Da / Num. of mol.: 1 / Fragment: 627- AND NLS-DOMAINS, RESIDUES 538-753 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 1 MICROLITRE OF 5.5 MG/ML PROTEIN SOLUTION IN 10 MM TRIS-HCL PH 7.0 AND 200 MM NACL WITH EQUAL VOLUME OF 100 MM HEPES PH 7.5 AND K/NA TARTRATE AT 1.2 M. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 14078 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.95 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.28 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 627-DOMAIN FROM PDB ENTRY 2VY7, AND NLS DOMAIN FROM PDB ENTRY 2JDQ Resolution: 1.95→26.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.993 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.179 / 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: 21.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.47 Å
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Refine LS restraints |
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