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SV40 Capsid Simplified
From Proteopedia
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| - | <applet load='Image:Sv40 capsid 360 atoms.pdb' size=' | + | <applet load='Image:Sv40 capsid 360 atoms.pdb' size='450' frame='true' align='right' caption='Simplified model of the SV40 virus capsid.' scene='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/4' /> |
| - | *<scene name='User:Eric_Martz/Sandbox_8/Sv40_front_half_cut_away/2'>Cut away front half</scene> | + | *<scene name='User:Eric_Martz/Sandbox_8/Sv40_front_half_cut_away/2'>Cut away front half</scene> (shows capsid only) |
*<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/4'>Restore Initial Scene</scene> | *<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/4'>Restore Initial Scene</scene> | ||
*<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/2'>Hide icosahedron</scene> | *<scene name='User:Eric_Martz/Sandbox_8/Initial_sv40_scene/2'>Hide icosahedron</scene> | ||
*<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> | ||
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| + | This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in [[1sva]]. | ||
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| + | 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 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. | ||
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| + | 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 [[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. | ||
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| + | Yellow-colored are the twelve 5-chain pentamers representing the 12 vertices that define the 20 equilateral triangle faces of the icosahedron. 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. | ||
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| + | {{Clear}} | ||
| + | <!-- requires more than default java memory! | ||
| + | ==Capsid Alpha Carbons Only== | ||
| + | <applet ' size='400' frame='true' align='right' caption='SV40 capsid as alpha carbon atoms only.' /> | ||
| + | Here may be shown the SV40 capsid as alpha carbon atoms only (126,420 atoms, 8.7 Mb; 2.6 Mb gzipped). The capsid with all non-hydrogen atoms is a 70 Mb file that exceeds the default memory allocated to java (and the [[Jmol]] applet). Because this is a very large file that <font color="red">'''may cause your browser to freeze or crash'''</font>, it is not displayed automatically. <scene name='SV40_Capsid_Simplified/Sv40_capsid_alpha_carbons_only/1'>Display SV40 Capsid (126,420 alpha carbon atoms)</scene>. Be patient! | ||
| + | --> | ||
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| + | ==Content Attribution== | ||
| + | The original contents of this page were adapted from a site developed for [[Chime]] in the [http://atlas.molviz.org Atlas of Macromolecules] with the permission of [[User:Eric Martz]]. | ||
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| + | ==Notes== | ||
| + | <references /> | ||
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| + | ==See Also== | ||
| + | * 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)". | ||
| + | <!-- | ||
| + | * The [http://firstglance.jmol.org/fg.htm?mol=http://proteopedia.org/wiki/images/1/1d/Sv40_capsid_360_atoms.pdb model in FirstGlance in Jmol]. NOT USEFUL! | ||
| + | * The atomic coordinate file [[Image:1sva-cao.mmol.gz]]. | ||
| + | --> | ||
Current revision
|
- (shows capsid only)
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 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.
In the highly simplified model at the right, each protein chain was reduced to a single atom, resulting in 360 atoms[1]. 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.
Yellow-colored are the twelve 5-chain pentamers representing the 12 vertices that define the 20 equilateral triangle faces of the icosahedron. 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.
Content Attribution
The original contents of this page were adapted from a site developed for Chime in the Atlas of Macromolecules with the permission of User:Eric Martz.
Notes
- ↑ Since each original chain of 1sva had ~2,700 non-hydrogen atoms, this reduced the size of the data by ~2,700 fold
See Also
- 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)".
