Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22951.39 
• Atom Count: 1515 
• Residue Count: 204 
• Unique protein chains: 1

3KC6

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

• DOI: 10.2210/pdb3KC6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2009-10-20 Released: 2010-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.245 
• R-Value Work: 0.202 

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

• PubMed: 20700447 
• DOI: 10.1371/journal.ppat.1001034
• Primary Citation of Related Structures:  
  3L56, 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Polymerase PB2	A	204	Influenza A virus	Mutation(s): 0  Gene Names: PB2
Find proteins for Q6DNN3 (Influenza A virus) Go to UniProtKB:  Q6DNN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.245 
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 33.084	α = 90.00
b = 65.696	β = 90.00
c = 96.855	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
StructureStudio	data collection
HKL-2000	data reduction
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-20 
• Released Date: 2010-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History 

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