6EUW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 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
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
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYB
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
YCNZDZZTLLGBPM-WAYYCVMKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description