6EVJ

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and capped RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.

Pflug, A.Gaudon, S.Resa-Infante, P.Lethier, M.Reich, S.Schulze, W.M.Cusack, S.

(2018) Nucleic Acids Res 46: 956-971

  • DOI: 10.1093/nar/gkx1210
  • Primary Citation of Related Structures:  
    6EUW, 6EUV, 6EUY, 6EUX, 6EVJ, 6EVK

  • PubMed Abstract: 
  • Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation ('priming state') and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA ...

    Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation ('priming state') and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA. In particular, mutation of PB2 Arg264, which interacts with the triphosphate linkage in the cap, significantly and specifically decreases cap-dependent transcription. We also compare the configuration of the midlink and cap-binding domains in the priming state with their very different relative arrangement (called the 'apo' state) in structures where the potent cap-binding inhibitor VX-787, or a close analogue, is bound. In the 'apo' state the inhibitor makes additional interactions to the midlink domain that increases its affinity beyond that to the cap-binding domain alone. The comparison suggests that the mechanism of resistance of certain mutations that allow virus to escape from VX-787, notably PB2 N510T, can only be rationalized if VX-787 has a dual mode of action, direct inhibition of capped RNA binding as well as stabilization of the transcriptionally inactive 'apo' state.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA, D738Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PA
Find proteins for H6QM92 (Influenza A virus)
Explore H6QM92 
Go to UniProtKB:  H6QM92
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB, E776Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for H6QM91 (Influenza A virus)
Explore H6QM91 
Go to UniProtKB:  H6QM91
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C, F809Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB2
Find proteins for H6QM90 (Influenza A virus)
Explore H6QM90 
Go to UniProtKB:  H6QM90
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')G [auth N], J [auth M]13synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')H [auth R], I [auth S]18Influenza A virus
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 6
        MoleculeChainsLengthOrganismImage
        RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*G)-3')K [auth U], L [auth V]16Influenza A virus
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.90 Å
        • R-Value Free: 0.245 
        • R-Value Work: 0.207 
        • R-Value Observed: 0.209 
        • Space Group: C 1 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 185.46α = 90
        b = 286.17β = 93.27
        c = 171.93γ = 90
        Software Package:
        Software NamePurpose
        REFMACrefinement
        XDSdata reduction
        XSCALEdata scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data

        • Deposited Date: 2017-11-01 
        • Released Date: 2017-12-13 
        • Deposition Author(s): Pflug, A., Cusack, S.

        Funding OrganizationLocationGrant Number
        European Research CouncilFrance322586

        Revision History  (Full details and data files)

        • Version 1.0: 2017-12-13
          Type: Initial release
        • Version 1.1: 2018-02-07
          Changes: Author supporting evidence, Database references, Source and taxonomy
        • Version 1.2: 2019-02-20
          Changes: Data collection, Source and taxonomy