3L56

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biological and structural characterization of a host-adapting amino acid in influenza virus.

Yamada, S.Hatta, M.Staker, B.L.Watanabe, S.Imai, M.Shinya, K.Sakai-Tagawa, Y.Ito, M.Ozawa, M.Watanabe, T.Sakabe, S.Li, C.Kim, J.H.Myler, P.J.Phan, I.Raymond, A.Smith, E.Stacy, R.Nidom, C.A.Lank, S.M.Wiseman, R.W.Bimber, B.N.O'Connor, D.H.Neumann, G.Stewart, L.J.Kawaoka, Y.

(2010) Plos Pathog. 6: e1001034-e1001034

  • DOI: 10.1371/journal.ppat.1001034
  • Primary Citation of Related Structures:  3KC6, 3KHW

  • PubMed Abstract: 
  • Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack ...

    Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack these amino acids. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals. Moreover, a basic amino acid at position 591 of PB2 substantially increased the lethality of an avian H5N1 virus in mice. We also present the X-ray crystallographic structure of the C-terminus of a pandemic H1N1 virus PB2 protein. Arginine at position 591 fills the cleft found in H5N1 PB2 proteins in this area, resulting in differences in surface shape and charge for H1N1 PB2 proteins. These differences may affect the protein's interaction with viral and/or cellular factors, and hence its ability to support virus replication in mammals.


    Organizational Affiliation

    Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase PB2
A, B
222Influenza A virus (A/Viet Nam/1203/2004(H5N1))Gene Names: PB2
Find proteins for Q6DNN3 (Influenza A virus (A/Viet Nam/1203/2004(H5N1)))
Go to UniProtKB:  Q6DNN3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.042α = 90.00
b = 57.007β = 102.40
c = 83.081γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
StructureStudiodata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2012-05-23
    Type: Database references