3HW6

Crystal structure of avian influenza virus PA_N in complex with Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center

Zhao, C.Lou, Z.Guo, Y.Ma, M.Chen, Y.Liang, S.Zhang, L.Chen, S.Li, X.Liu, Y.Bartlam, M.Rao, Z.

(2009) J.Virol. 83: 9024-9030

  • DOI: 10.1128/JVI.00911-09
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Highly pathogenic influenza virus strains currently in circulation pose a significant risk of a global pandemic. Following the reported crystal structure of the endonuclease domain from the avian influenza virus polymerase PA subunit, here we report ...

    Highly pathogenic influenza virus strains currently in circulation pose a significant risk of a global pandemic. Following the reported crystal structure of the endonuclease domain from the avian influenza virus polymerase PA subunit, here we report the results of a systematic X-ray crystallographic analysis of its complex with adenosine, uridine, and thymidine nucleoside monophosphates (NMPs). Electron density corresponding to the monophosphate moiety of each nucleotide was apparent in each NMP complex and bound to the catalytic metal. A hydrophobic site was found to contribute to nucleoside binding. The NMP complex structures should represent the conformation of the bound product after nuclease cleavage. Moreover, one solvent molecule was found to occupy an equivalent position to the second reported Mn(2+) ion, where it mediates the interaction between bound NMPs and the N-terminal PA domain in the presence of the Mg(2+) ion. The results presented here indicate a possible cleavage mechanism and identify a distinct nucleotide binding pocket. The identification of this binding pocket opens a new avenue for anti-influenza drug discovery, targeting the cap-dependent endonuclease, in response to the worldwide threat of influenza.


    Organizational Affiliation

    Laboratory of Structural Biology, Room 201, New Life Sciences Building, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A, B, C, D
261Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q9Q0U9 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9Q0U9
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.504α = 96.06
b = 60.211β = 96.49
c = 67.215γ = 109.66
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance