SV40 Capsid Simplified: Difference between revisions
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*<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/3'>Hide capsid</scene> | *<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/3'>Hide capsid</scene> | ||
This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published | This model is based on the crystallographic solution of the VP1 capsid protein of [https://en.wikipedia.org/wiki/SV40 Simian Virus 40], published as [[1sva]] in 1996<ref>PMID: 8805523</ref>. SV40 is a member of a group of cancer-causing viruses that has been extensively researched for decades. | ||
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. | 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. | ||
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[[FirstGlance in Jmol]], since August, 2022, automatically constructs the capsid from the [[asymmetric unit]] of [[1sv4]], and automatically simplifies it to < 25,000 atoms to enable [[JSmol]] to handle it smoothly. | [[FirstGlance in Jmol]], since August, 2022, automatically constructs the capsid from the [[asymmetric unit]] of [[1sv4]], and automatically simplifies it to < 25,000 atoms to enable [[JSmol]] to handle it smoothly. | ||
<big>[http://firstglance.jmol.org/fg.htm?mol=1sva See less-simplified SV40 capsid].</big> | <big>[http://firstglance.jmol.org/fg.htm?mol=1sva See less-simplified SV40 capsid in FirstGlance in Jmol].</big> | ||
In the Views tab of FirstGlance, click Slab, and then check both of the checkboxes in the Slab options. You will get a result similar to the animation below. Can you pick out vertices with 5 and others with 6 nearest neighbors? | In the Views tab of FirstGlance, click Slab, and then check both of the checkboxes in the Slab options. You will get a result similar to the animation below. Can you pick out vertices with 5 and others with 6 nearest neighbors? | ||
