PB2 is one of four proteins which make up the influenza A virus replication complex. This complex is responsible for the synthesis of both genomic and messenger viral RNA, the hereditary and infective agents of the flu virus. The polymerase complex is also a determinant of both host specificity and pathogenicity, in other words it helps determine who gets sick and by how much. We have compared structural features of bird H5N1 flu virus with swine H1N1 flu virus. Typically, the presence of two amino acids -- lysine and asparagine -- at specific sites on the PB2 protein, are required for a bird flu virus to make the jump from its avian host to replicate efficiently in human cells. However, the swine flu H1N1 virus lacked both of these amino acid building blocks. The structural data compiled by SSGCID reveals changes in the surface shape of the swine H1N1 virus PB2 protein compared to that of the avian PB2, differences which could, in turn, affect factors in the human cell that would otherwise inhibit virus replication. The structural data has been published together with biological data from the group of Dr. Yoshihiro Kawaoka of the University of Wisconsin-Madison's School of Veterinary Medicine. Dr. Kawaoka and collaborators found that changes in amino acid residues (mutations) located on the surface of the “PB2” polymerase protein are responsible for the H1N1 virus' ability to adapt to and co-opt human cells.
For more information, please see the Protein Data Bank entries 3KC6, 3KHW and 3L56. The Structure shown is for PB2 from Influenza A virus strain A/Mexico/InDRE4487/2009(H1N1). See also publication by Yamada et al. (PLoS Pathogens 5;6(8) (2010) PDF).