5CGV

2009 H1N1 PA endonuclease in complex with L-742,001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor.

Song, M.S.Kumar, G.Shadrick, W.R.Zhou, W.Jeevan, T.Li, Z.Slavish, P.J.Fabrizio, T.P.Yoon, S.W.Webb, T.R.Webby, R.J.White, S.W.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: 3669-3674

  • DOI: 10.1073/pnas.1519772113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The influenza endonuclease is an essential subdomain of the viral RNA polymerase. It processes host pre-mRNAs to serve as primers for viral mRNA and is an attractive target for antiinfluenza drug discovery. Compound L-742,001 is a prototypical endonu ...

    The influenza endonuclease is an essential subdomain of the viral RNA polymerase. It processes host pre-mRNAs to serve as primers for viral mRNA and is an attractive target for antiinfluenza drug discovery. Compound L-742,001 is a prototypical endonuclease inhibitor, and we found that repeated passaging of influenza virus in the presence of this drug did not lead to the development of resistant mutant strains. Reduced sensitivity to L-742,001 could only be induced by creating point mutations via a random mutagenesis strategy. These mutations mapped to the endonuclease active site where they can directly impact inhibitor binding. Engineered viruses containing the mutations showed resistance to L-742,001 both in vitro and in vivo, with only a modest reduction in fitness. Introduction of the mutations into a second virus also increased its resistance to the inhibitor. Using the isolated wild-type and mutant endonuclease domains, we used kinetics, inhibitor binding and crystallography to characterize how the two most significant mutations elicit resistance to L-742,001. These studies lay the foundation for the development of a new class of influenza therapeutics with reduced potential for the development of clinical endonuclease inhibitor-resistant influenza strains.


    Organizational Affiliation

    Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
187Influenza A virus (strain swl A/California/04/2009 H1N1)Mutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Go to UniProtKB:  C3W5S0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
0N8
Query on 0N8

Download SDF File 
Download CCD File 
A
(2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid
C23 H24 Cl N O4
DGJZJCIAWLMRBY-ZHZULCJRSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0N8IC50: 480 nM (86) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.199 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.899α = 90.00
b = 73.899β = 90.00
c = 127.457γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-09 
  • Released Date: 2016-03-23 
  • Deposition Author(s): Kumar, G., White, S.W.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI098757
St. Jude Children's Research HospitalUnited States--
ALSACUnited States--

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references