SV40 Capsid Simplified: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| Line 10: | Line 10: | ||
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. | 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 [[ | 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_modeling_and_visualization_software|molecular visualization programs]]) to display the model easily, with overlapping "atomic" spheres to simulate the capsid. | ||
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. | 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. | ||