4E5G

Crystal structure of avian influenza virus PAn bound to compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.647 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease.

Dubois, R.M.Slavish, P.J.Baughman, B.M.Yun, M.K.Bao, J.Webby, R.J.Webb, T.R.White, S.W.

(2012) Plos Pathog. 8: e1002830-e1002830

  • DOI: 10.1371/journal.ppat.1002830
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral rep ...

    Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral replication. Translation of viral mRNAs by the host ribosome requires mRNA capping for recognition and binding, and the necessary mRNA caps are cleaved or "snatched" from host pre-mRNAs by the PA endonuclease. The structure-based development of inhibitors that target PA endonuclease is now possible with the recent crystal structure of the PA catalytic domain. In this study, we sought to understand the molecular mechanism of inhibition by several compounds that are known or predicted to block endonuclease-dependent polymerase activity. Using an in vitro endonuclease activity assay, we show that these compounds block the enzymatic activity of the isolated PA endonuclease domain. Using X-ray crystallography, we show how these inhibitors coordinate the two-metal endonuclease active site and engage the active site residues. Two structures also reveal an induced-fit mode of inhibitor binding. The structures allow a molecular understanding of the structure-activity relationship of several known influenza inhibitors and the mechanism of drug resistance by a PA mutation. Taken together, our data reveal new strategies for structure-based design and optimization of PA endonuclease inhibitors.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase protein PA
A, B, C, D
187Influenza A virusMutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q5EP34 (Influenza A virus)
Go to UniProtKB:  Q5EP34
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
XI7
Query on XI7

Download SDF File 
Download CCD File 
A, B, C, D
2-4-DIOXO-4-PHENYLBUTANOIC ACID
C10 H8 O4
JGKFWCXVYCDKDU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XI7IC50: 21300 nM (86) BINDINGDB
XI7EC50: 2070 nM (86) BINDINGDB
XI7Ki: 480 nM (86) BINDINGDB
XI7IC50: 21300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.647 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.243 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 126.892α = 90.00
b = 133.659β = 90.00
c = 126.778γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy