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Yorodumi- PDB-6f5o: A mechanism for the activation of the influenza virus transcriptase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f5o | ||||||||||||
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Title | A mechanism for the activation of the influenza virus transcriptase | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / influenza virus RNA dependent RNA polymerase | ||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / viral transcription / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / viral transcription / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.8 Å | ||||||||||||
Authors | Serna Martin, I. / Grimes, J.M. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Mol Cell / Year: 2018 Title: A Mechanism for the Activation of the Influenza Virus Transcriptase. Authors: Itziar Serna Martin / Narin Hengrung / Max Renner / Jane Sharps / Mónica Martínez-Alonso / Simonas Masiulis / Jonathan M Grimes / Ervin Fodor / Abstract: Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For ...Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For transcription, FluPol interacts with the C-terminal domain (CTD) of RNA polymerase II (Pol II), which enables FluPol to snatch capped RNA primers from nascent host RNAs. Here, we describe the co-crystal structure of influenza C virus polymerase (FluPol) bound to a Ser5-phosphorylated CTD (pS-CTD) peptide. The position of the CTD-binding site at the interface of PB1, P3, and the flexible PB2 C-terminal domains suggests that CTD binding stabilizes the transcription-competent conformation of FluPol. In agreement, both cap snatching and capped primer-dependent transcription initiation by FluPol are enhanced in the presence of pS-CTD. Mutations of amino acids in the CTD-binding site reduce viral mRNA synthesis. We propose a model for the activation of the influenza virus transcriptase through its association with pS-CTD of Pol II. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6f5o.cif.gz | 452 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f5o.ent.gz | 370 KB | Display | PDB format |
PDBx/mmJSON format | 6f5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/6f5o ftp://data.pdbj.org/pub/pdb/validation_reports/f5/6f5o | HTTPS FTP |
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-Related structure data
Related structure data | 4190MC 6f5pC M: map data used to model this data 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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-Components
#1: Protein | Mass: 83232.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Gene: PA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5V8Z9 |
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#2: Protein | Mass: 84433.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase |
#3: Protein | Mass: 88028.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5V8X3 |
#4: RNA chain | Mass: 4321.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus (B/Memphis/13/2003) |
#5: RNA chain | Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus (B/Memphis/13/2003) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Influenza C virus polymerase bound to promoter vRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Influenza B virus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 2.09 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9159 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |