Surface rendering of the virus particle (top left):
This is a surface rendering of the capsid based on the atomic
coordinates created using the TexMol software
(http://www.ices.utexas.edu/CCV). The colors are depth cued along a
color gradient: yellow at a larger radius,
and greenish blue as the radius decreases. This rendering is
designed to give an impression similar
to that of a cryo electron microscopy reconstruction at 10 Å
surface topology is readily seen with large-scale features such
as "canyons", "mountain
tops", and distinctive morphological units (e.g. hexamers and
pentamers) readily visible.
It is convenient to compare virus particles with this rendering
because if you click
on the image, an image appears that is scaled with all other
viruses that are presented
in the site. Thus it is possible to create a gallery of viruses
that are scaled to
each other by combining these images for all the viruses. Visit
Gallery Maker to easily create such a gallery.
Ribbon drawing of the subunit(s) and Icos. asymmetric unit
A ribbon drawing is provided for each of the unique gene products
in the viral capsid.
For a quasi-equivalent virus made of multiple copies of a single
gene product, only one
of the copies is shown. For picornavirus and related capsids
there will be three
ß sandwich domains. The ribbon drawings are colored with
continuously through the spectrum from blue at the N-terminus to
red at the C-terminus.
Strands of ß-sheets are depicted as arrows pointing in the
direction of increasing
sequence and helices are formed as coiled ribbons. Regions
without a distinct secondary
structure are depicted as a tube.
Schematic description of the capsid in the context of an
icosahedral lattice(upper right):
All of the viral capsids in this database display icosahedral
symmetry. Some of the particles
have the shape of an icosahedron, while others conform to the
shape of other geometric solids
that display icosahedral symmetry. These may include a truncated
rhombic triacontahedron, or a dodecahedron. This figure shows a
CA trace of the subunits illustrating the shape of the subunit in the
context of an icosahedral lattice superposed on it. In addition, each
subunit is identified by a number (e..g, A1, B2, ..) for the purposes
of calculations of association energies and inter-subunit contacts.
The fidelity of
some viruses to these shapes is remarkable with dihedral angles
between subunits conforming
to within experimental error to the dihedral angles required to
form the geometric solid.
Subunit organization, shown as tube representation of the
subunits (bottom right):
This drawing shows the detailed association of subunit C-alpha
backbones to illustrate
the dominant interactions within the particle. Different types of
subunits are shown in different colors.