Influenza A and B viruses are major causes of seasonal flu epidemics each year. Hemagglutinin (HA) mediates the binding of virus to host cell and the fusion with host membrane. The crystal of HA in complex with antibody that reveals the mechanism by which antibody recognizes HA may not diffract to high resolution, thereby preventing the accurate interpretation of the structural model. The application of normal mode refinement that aims for improving the structure quality at the low resolution is tested. These studies provide some guidelines for future refinement of HA-antibody complex structures. By comparing the residues constituting the base of the receptor binding site of influenza A and B virus HAs, it is found that they share some similarities, except for a Phe at position 95 of influenza B virus hemagglutinin (BHA) versus Tyr in of influenza A virus hemagglutinin (AHA). The recombinant protein BHA containing the F95Y mutation exhibits the increased receptor binding affinity and specificity. However, recombinant viruses with the Phe95Tyr mutation show lower erythrocyte agglutination titer and decreased binding abilities with different cell lines. The replication of the Phe95Tyr mutant virus in mice is also attenuated. These data suggest that the increased receptor binding ability of HA alone is not advantageous to the pathogenesis of the viruses. The structure of BHA2 (a portion of BHA near the C-terminus) at the post-fusion state has been determined to 2.45 Å resolution. This protein forms a hairpin-like conformation rich in -helices. About 70 residues from the N-terminus is a three-stranded coiled coil, and the remaining of the protein packs in anti-parallel against the groove formed by the central helices. In the post-fusion state of BHA2, the helix converted from the B-loop in pre-fusion state contacts the C-terminal fragment of this protein with more hydrophobic interactions as compared to AHA2. This structure illustrates the distinct stabilization strategy employed by BHA2 to form a post-fusion state that resembles that for AHA2. These studies will further the understanding of BHA with respect to its role in receptor binding ability and fusion.