6EUX

Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 consiste ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
A
292Influenza B virusMutation(s): 0 
Gene Names: PB2
Find proteins for Q5V8X3 (Influenza B virus)
Go to UniProtKB:  Q5V8X3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BYB
Query on BYB

Download SDF File 
Download CCD File 
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
YCNZDZZTLLGBPM-WAYYCVMKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.200α = 90.00
b = 73.200β = 90.00
c = 103.740γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-31 
  • Released Date: 2017-12-13 
  • Deposition Author(s): Cusack, S., Gaudon, S.

Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History 

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