SV40 Capsid Simplified: Difference between revisions
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This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in [[1sva]] in 1996. | This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in [[1sva]] in 1996. | ||
The [[asymmetric unit]] of [[1sva]] contains a pentamer of the VP1 protein plus one extra chain. In about 2010, the entire capsid was constructed from 1sva by the (now defunct) 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 vertices forming 20 equilateral triangle faces). The PDB atomic coordinate file for the capsid, containing all non-hydrogen protein atoms, is 70 megabytes in size with about one million atoms, and 123,420 alpha carbon atoms. | The [[asymmetric unit]] of [[1sva]] contains a pentamer of the VP1 protein plus one extra chain. In about 2010, the entire capsid was constructed from 1sva by the (now defunct) 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 [https://en.wikipedia.org/wiki/Regular_icosahedron icosahedron] (12 vertices forming 20 equilateral triangle faces). The PDB atomic coordinate file for the capsid, containing all non-hydrogen protein atoms, is 70 megabytes in size with about one million atoms, and 123,420 alpha carbon atoms. | ||
In the highly simplified model at the right, '''each protein chain was reduced to a single atom''', resulting in 360 atoms<ref>Since each original chain of [[1sva]] had ~2,700 non-hydrogen atoms, this reduced the size of the data by ~2,700 fold</ref>. The distances between atoms were then greatly reduced to enable early versions of [[Jmol]] (and other common [[Molecular_modeling_and_visualization_software|molecular visualization programs]]) to display the model more easily, with overlapping "atomic" spheres to simulate the capsid. | In the highly simplified model at the right, '''each protein chain was reduced to a single atom''', resulting in 360 atoms<ref>Since each original chain of [[1sva]] had ~2,700 non-hydrogen atoms, this reduced the size of the data by ~2,700 fold</ref>. The distances between atoms were then greatly reduced to enable early versions of [[Jmol]] (and other common [[Molecular_modeling_and_visualization_software|molecular visualization programs]]) to display the model more easily, with overlapping "atomic" spheres to simulate the capsid. | ||