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Yorodumi- PDB-8bf5: Early transcription elongation state of influenza A/H7N9 polymera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bf5 | |||||||||
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Title | Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza / viral RNA-dependent RNA polymerase / cap-dependent transcription / nucleoside analogue | |||||||||
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 / viral transcription / host cell mitochondrion / 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 / viral transcription / host cell mitochondrion / 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: 2.96 Å | |||||||||
Authors | Cusack, S. / Kouba, T. | |||||||||
Funding support | France, 1items
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Citation | Journal: Cell Rep / Year: 2023 Title: Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106. Authors: Tomas Kouba / Anna Dubankova / Petra Drncova / Elisa Donati / Pietro Vidossich / Valentina Speranzini / Alex Pflug / Johanna Huchting / Chris Meier / Marco De Vivo / Stephen Cusack / Abstract: The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although ...The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the +1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bf5.cif.gz | 838.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bf5.ent.gz | 694.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bf5 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bf5 | HTTPS FTP |
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-Related structure data
Related structure data | 16013MC 7qtlC 7r0eC 7r1fC 7zplC 7zpmC 8bdrC 8be0C 8bekC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 85822.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PA / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 86207.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase |
#3: Protein | Mass: 90844.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Strain: B/Memphis/13/2003 / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3 |
-RNA chain , 3 types, 3 molecules VRM
#4: RNA chain | Mass: 4495.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus |
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#5: RNA chain | Mass: 6706.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus |
#6: RNA chain | Mass: 5945.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus |
-Non-polymers , 3 types, 5 molecules
#7: Chemical | #8: Chemical | ChemComp-G2P / | #9: Chemical | ChemComp-GTA / | |
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-Details
Has ligand of interest | Y |
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-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: Early transcription elongation state of influenza A/H7N9 polymerase stalled with incoming GTP analogue Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.255 MDa / Experimental value: NO |
Source (natural) | Organism: Influenza B virus (B/Memphis/13/2003) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55634 / Symmetry type: POINT | ||||||||||||||||||||||||
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