Crystal structure of the cap-binding domain of the PB2 subunit of influenza A/H5N1 polymerase bound to an azaindazole inhibitor

Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2163Influenza A virus (A/duck/Shantou/4610/2003(H5N1))Mutation(s): 3 
Gene Names: PB2
Find proteins for Q2LG68 (Influenza A virus)
Explore Q2LG68 
Go to UniProtKB:  Q2LG68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2LG68
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BYB

Download Ideal Coordinates CCD File 
B [auth A](2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid
C19 H18 F2 N6 O2
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
BYB Binding MOAD:  6EUW Kd: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.49α = 90
b = 62.49β = 90
c = 69.97γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

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