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Yorodumi- PDB-5d98: Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d98 | ||||||||||||||||||
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Title | Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212 | ||||||||||||||||||
Components |
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Keywords | TRANSFERASE/RNA / RNA-dependent RNA polymerase / Influenza / Influenza C virus / Negative-strand virus / transferase-RNA complex | ||||||||||||||||||
Function / homology | Function and homology information viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cap snatching / 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 / DNA-templated transcription / nucleotide binding / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Influenza C virus | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.9 Å | ||||||||||||||||||
Authors | Hengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Nature / Year: 2015 Title: Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Authors: Hengrung, N. / El Omari, K. / Serna Martin, I. / Vreede, F.T. / Cusack, S. / Rambo, R.P. / Vonrhein, C. / Bricogne, G. / Stuart, D.I. / Grimes, J.M. / Fodor, E. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d98.cif.gz | 858.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d98.ent.gz | 718.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d98_validation.pdf.gz | 499.2 KB | Display | wwPDB validaton report |
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Full document | 5d98_full_validation.pdf.gz | 578.1 KB | Display | |
Data in XML | 5d98_validation.xml.gz | 149.5 KB | Display | |
Data in CIF | 5d98_validation.cif.gz | 198.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/5d98 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/5d98 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 82025.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966) Gene: PA, P3 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP5 #2: Protein | Mass: 86145.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966) Gene: PB1 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP4, RNA-directed RNA polymerase #3: Protein | Mass: 88972.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza C virus (strain C/Johannesburg/1/1966) Gene: PB2 / Plasmid: MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IMP3 #4: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.21 Å3/Da / Density % sol: 76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ...Details: Drops were set up by mixing polymerase (5.8 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 70% Morpheus G2 (10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M carboxylic acids (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium l-tartrate, 0.2 M sodium oxamate), 0.1 M MES/imidazole) in a 2:1 protein:precipitant ratio. |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.9→100.57 Å / Num. obs: 95267 / % possible obs: 98.8 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.2 | |||||||||||||||
Reflection shell | Resolution: 3.9→4 Å / Redundancy: 20.6 % / Rmerge(I) obs: 3.685 / Mean I/σ(I) obs: 1.3 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3.9→50.01 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 80.769 / SU ML: 0.987 / Cross valid method: THROUGHOUT / ESU R Free: 0.805 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 205.572 Å2
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Refinement step | Cycle: 1 / Resolution: 3.9→50.01 Å
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Refine LS restraints |
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