6FS7

Influenza A/California/04/2009 (pH1N1) endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil.

Omoto, S.Speranzini, V.Hashimoto, T.Noshi, T.Yamaguchi, H.Kawai, M.Kawaguchi, K.Uehara, T.Shishido, T.Naito, A.Cusack, S.

(2018) Sci Rep 8: 9633-9633

  • DOI: 10.1038/s41598-018-27890-4
  • Primary Citation of Related Structures:  
    6FSB, 6FS6, 6FS8, 6FS7, 6FS9

  • PubMed Abstract: 
  • Baloxavir acid (BXA), derived from the prodrug baloxavir marboxil (BXM), potently and selectively inhibits the cap-dependent endonuclease within the polymerase PA subunit of influenza A and B viruses. In clinical trials, single doses of BXM profoundly decrease viral titers as well as alleviating influenza symptoms ...

    Baloxavir acid (BXA), derived from the prodrug baloxavir marboxil (BXM), potently and selectively inhibits the cap-dependent endonuclease within the polymerase PA subunit of influenza A and B viruses. In clinical trials, single doses of BXM profoundly decrease viral titers as well as alleviating influenza symptoms. Here, we characterize the impact on BXA susceptibility and replicative capacity of variant viruses detected in the post-treatment monitoring of the clinical studies. We find that the PA I38T substitution is a major pathway for reduced susceptibility to BXA, with 30- to 50-fold and 7-fold EC 50 changes in A and B viruses, respectively. The viruses harboring the I38T substitution show severely impaired replicative fitness in cells, and correspondingly reduced endonuclease activity in vitro. Co-crystal structures of wild-type and I38T influenza A and B endonucleases bound to BXA show that the mutation reduces van der Waals contacts with the inhibitor. A reduced affinity to the I38T mutant is supported by the lower stability of the BXA-bound endonuclease. These mechanistic insights provide markers for future surveillance of treated populations.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France. cusack@embl.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic protein,Polymerase acidic proteinA, B, C, D, E, F193Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 1 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S0 
Go to UniProtKB:  C3W5S0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E4Z (Subject of Investigation/LOI)
Query on E4Z

Download Ideal Coordinates CCD File 
I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]Baloxavir acid
C24 H19 F2 N3 O4 S
FIDLLEYNNRGVFR-CTNGQTDRSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , P [auth D] , Q [auth D] , 
G [auth A],  H [auth A],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  P [auth D],  Q [auth D],  S [auth E],  T [auth E],  V [auth F],  W [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.68α = 90
b = 75.56β = 90
c = 121.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release