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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1093/nar/gkx1210
  • Primary Citation of Related Structures:  
    6EUV, 6EUW, 6EUX, 6EUY, 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. 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein
A, D
738Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PA
UniProt
Find proteins for H6QM92 (Influenza A virus)
Explore H6QM92 
Go to UniProtKB:  H6QM92
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UniProt GroupH6QM92
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit
B, E
776Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for H6QM91 (Influenza A virus)
Explore H6QM91 
Go to UniProtKB:  H6QM91
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UniProt GroupH6QM91
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2
C, F
809Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for H6QM90 (Influenza A virus)
Explore H6QM90 
Go to UniProtKB:  H6QM90
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UniProt GroupH6QM90
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-D(*(GDM))-R(P*AP*AP*U)-3')G [auth N],
J [auth M]
13synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
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
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Entity ID: 6
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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  • Reference Sequence
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

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Entry History & Funding Information

Deposition Data


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
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-02-28
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary