6WS3

The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomers TG and AGCA (from cleaved GTGAGCAGTG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.

Kumar, G.Cuypers, M.Webby, R.R.Webb, T.R.White, S.W.

(2021) Nucleic Acids Res 49: 1609-1618

  • DOI: https://doi.org/10.1093/nar/gkaa1294
  • Primary Citation of Related Structures:  
    6W7A, 6WHM, 6WS3, 7KAF, 7KBC, 7KL3

  • PubMed Abstract: 

    The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN) of the influenza RNA dependent RNA polymerase, and we report here complexes of PAN with RNA and DNA oligonucleotides to understand its specificity and the structural basis of baloxavir resistance mutations. The RNA and DNA oligonucleotides bind within the substrate binding groove of PAN in a similar fashion, explaining the ability of the enzyme to cleave both substrates. The individual nucleotides occupy adjacent conserved pockets that flank the two-metal active site. However, the 2' OH of the RNA ribose moieties engage in additional interactions that appear to optimize the binding and cleavage efficiency for the natural substrate. The major baloxavir resistance mutation at position 38 is at the core of the substrate binding site, but structural studies and modeling suggest that it maintains the necessary virus fitness via compensating interactions with RNA. These studies will facilitate the development of new influenza therapeutics that spatially match the substrate and are less likely to elicit resistance mutations.


  • Organizational Affiliation

    Department of Structural Biology, Memphis, TN 38105, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PA-X,Polymerase acidic protein197Influenza A virusInfluenza A virus (A/Luxembourg/43/2009(H1N1))
This entity is chimeric
Mutation(s): 0 
Gene Names: PA-XPA
UniProt
Find proteins for C6H0Y9 (Influenza A virus)
Explore C6H0Y9 
Go to UniProtKB:  C6H0Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6H0Y9
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*G)-3')B [auth F],
C [auth E]
10synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.646α = 90
b = 89.646β = 90
c = 133.773γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description