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Yorodumi- PDB-7zpl: Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zpl | ||||||
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Title | Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook | ||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza / H7N9 / viral RNA-dependent RNA polymerase | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 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 | 7zpl.cif.gz | 529.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zpl.ent.gz | 409.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zpl ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zpl | HTTPS FTP |
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-Related structure data
Related structure data | 14857MC 7qtlC 7r0eC 7r1fC 7zpmC 8bdrC 8be0C 8bekC 8bf5C M: map data used to model this data C: citing same article (ref.) |
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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
#1: Protein | Mass: 82930.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Production host: Trichoplusia ni (cabbage looper) References: UniProt: M9TI86, Hydrolases; Acting on ester bonds #2: Protein | Mass: 86496.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: M9TLW3, RNA-directed RNA polymerase #3: Protein | Mass: 86007.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSK TNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQ ...Details: MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSK TNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQ DVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRIS SSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIV AMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENV KIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNV RGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) Strain: A/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: X5F427 #4: RNA chain | Mass: 4557.820 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) #5: Chemical | ChemComp-MG / | Has ligand of interest | N | |
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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: Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Value: 0.51 MDa / Experimental value: NO |
Source (natural) | Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS 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: 3000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 48 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 AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58775 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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