SV40 Capsid Simplified
This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in 1sva.
The asymmetric unit of 1sva contains a pentamer of the VP1 protein plus one extra chain. The entire capsid was constructed from 1sva by the Probable Quaternary Structure server (of the European Bioinformatics Institute) using symmetry operations specified in 1sva.pdb (REMARK 350). The resulting capsid model contains 360 chains of VP1 protein arranged as 72 pentamers in an icosahedron (12 faces). The PDB atomic coordinate file for the capsid, containing all non-hydrogen protein atoms, is 70 megabytes in size.
In the highly simplified model at the right, each protein chain was reduced to a single atom, resulting in 360 atoms. The distances between atoms were then greatly reduced to enable Jmol (and other common molecular visualization programs) to display the model more easily, with overlapping "atomic" spheres to simulate the capsid.
5-chain pentamers representing the vertices that define the 12 faces of the icosahedron are colored yellow. Pseudoatoms were placed over each vertex to enable drawing lines representing the orientation of the icosahedron. Notice that each yellow 5-chain pentamer is surrounded by five pentamers, while each gray pentamer is surrounded by six pentamers.
- ↑ Since each original chain of 1sva had ~2,700 non-hydrogen atoms, this reduced the size of the data by ~2,700 fold
- The atomic coordinate file Image:Sv40 capsid 360 atoms.pdb. The capsid atoms are "chain V"; the icosahedron atoms are "chain I"; and the vertex atoms (yellow above) can be selected as "select 2". Pseudobonds were generated between the vertex atoms in Jmol with "connect 2 (:i) (:i)".