The difference of the mean from the peak value is due to the long tails of the distribution for large distances Ibrutinib that are the effect of small gaps in the glycoprotein positions. The HA glycoproteins are 70 Å at their widest and are therefore well-separated on average and not in contact at their ectodomains. Based on our models of the HAs, we calculate the fractional volume occupied by the glycoproteins on the surface, defined here as a layer beyond the membrane one HA molecule thick. The fractional volume values for the three X-31 virions reported

in Fig. 3 are 13.5%, 15.0%, and 15.5% and for the three Udorn virions, 15.2%, 16.8%, and 19.2%. The fraction of the membrane surface area that the HA covers in projection is roughly twice the volume fraction value, and reflects the fact that the HA deviates from a cylinder in shape so that the head domain hides volume close to the membrane. Fig. 4a shows a model for the glycoprotein positions on one surface of an X-31 virion with a fractional volume of 13%. The surface is surprisingly open in contrast

Panobinostat research buy to the impression from viewing the virus in projection images. Because the HA is recognized by neutralizing antibodies, we considered which parts of the protein are accessible to antibodies in the context of the virus surface. While the sequence variable head domain is likely to be exposed, one consequence of the open packing is that epitopes near the membrane

are accessible. Fig. 4c shows the previously described crystal structure [7] of the HA in complex with an Fab from the broadly neutralizing antibody FI6 that recognizes an epitope in the stem domain. In Fig. 4a, several HA positions are shown where there is enough room for 3 Fabs to bind a single HA without clashing into another HA position. Fig. 4b shows a Udorn surface of slightly higher fractional volume (15%). Several positions are also shown because where there is enough room for an HA to bind a single Fab, and typically each glycoprotein can be oriented to bind at least one Fab. Though we have assessed the locations where Fabs can bind using a rigid Fab model, when the known flexibility of the Fab is considered, there are likely to be even fewer constraints on binding the stem region. A striking feature of the virus particles is the curvature of the membrane. For capsule or filament-shaped viruses of the most typical dimension in our preparations, the virus has a small radius of curvature perpendicular to the long axis of the capsule (Fig. 5). One consequence of this curvature would be a geometric constraint on the fraction of the virus surface that could engage with receptors on a target surface. The receptor binding site is located near the top of the HA as shown by the purple ligand in Fig. 4c. We calculate the relative distance of the receptor binding sites (Fig.