6QCW

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural snapshots of actively transcribing influenza polymerase.

Kouba, T.Drncova, P.Cusack, S.

(2019) Nat Struct Mol Biol 26: 460-470

  • DOI: 10.1038/s41594-019-0232-z
  • Primary Citation of Related Structures:  
    6QCX, 6QCS, 6QCT, 6QCW, 6QCV

  • PubMed Abstract: 
  • Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA ...

    Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France. cusack@embl.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA751Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for Q5V8Z9 (Influenza B virus)
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Go to UniProtKB:  Q5V8Z9
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB772Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for Q5V8Y6 (Influenza B virus)
Explore Q5V8Y6 
Go to UniProtKB:  Q5V8Y6
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C798Influenza B virus (B/Memphis/13/2003)Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q5V8X3 (Influenza B virus)
Explore Q5V8X3 
Go to UniProtKB:  Q5V8X3
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*CP*AP*UP*AP*AP*UP*AP*G)-3')D [auth M]15synthetic construct
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-3')E [auth R]21synthetic construct
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 6
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3')F [auth V]14synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PO4
      Query on PO4

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth B], I [auth B]PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.88 Å
      • R-Value Free: 0.234 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.215 
      • Space Group: P 32 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 200.354α = 90
      b = 200.354β = 90
      c = 256.466γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      AutoPROCdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      European CommissionFrance322586
      French National Research AgencyFranceANR-18-CE11-0028

      Revision History  (Full details and data files)

      • Version 1.0: 2019-06-05
        Type: Initial release
      • Version 1.1: 2019-06-12
        Changes: Data collection, Database references
      • Version 1.2: 2019-06-19
        Changes: Data collection, Database references