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Yorodumi- PDB-5epi: CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5epi | ||||||
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Title | CRYSTAL STRUCTURE OF INFLUENZA B POLYMERASE WITH BOUND 5' CRNA EXHIBITS A NOVEL DOMAIN ARRANGEMENT | ||||||
Components |
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Keywords | TRANSFERASE / INFLUENZA B VIRUS / RNA-DEPENDENT RNA POLYMERASE / HETEROTRIMER / SUBUNITS PA / PB1 / PB2 / VIRAL RNA / CRNA 5' END / INFLUENZA | ||||||
Function / homology | Function and homology information 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 | Influenza B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å | ||||||
Authors | Guilligay, D. / Cusack, S. | ||||||
Funding support | France, 1items
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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. #1: Journal: To Be Published Title: Crystal Structure Of Influenza A Polymerase Bound To The Viral RNA Promoter Authors: Reich, S. / Guilligay, D. / Pflug, A. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5epi.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5epi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5epi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5epi ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5epi | HTTPS FTP |
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-Related structure data
Related structure data | 5fmlC 5fmmC 5fmqC 5fmzC 4wsaS 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 85822.781 Da / Num. of mol.: 6 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 B virus (B/Memphis/13/2003) / Gene: PA / Plasmid: PKL-PBAC / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Z9 #2: Protein | Mass: 86207.016 Da / Num. of mol.: 6 / Fragment: PB1 SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PB1 / Plasmid: PKL-PBAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase #3: Protein | Mass: 90858.133 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PB2 / Plasmid: PKL-PBAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3 #4: RNA chain | Mass: 3921.464 Da / Num. of mol.: 6 / Fragment: FIRST 12 NUCLEOTIDES / Source method: obtained synthetically / Source: (synth.) Influenza B virus (B/Memphis/13/2003) Sequence details | N-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL ...N-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE. N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER, STREP-TAG AND TEV SITE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100 MM TRI SODIUM CITRATE PH 5.6, 10 OR 100 MM NACL AND 12% MPD PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07228 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07228 Å / Relative weight: 1 |
Reflection | Resolution: 4.1→50 Å / Num. obs: 195792 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.49 |
Reflection shell | Resolution: 4.1→4.3 Å / Redundancy: 1.77 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.23 / % possible all: 94.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSA Resolution: 4.1→49.945 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.77 / 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: LAST / Resolution: 4.1→49.945 Å
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Refine LS restraints |
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LS refinement shell |
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