SV40 Capsid Simplified - Revision history

Eric Martz at 23:36, 8 March 2022

Eric Martz — Tue, 08 Mar 2022 23:36:27 GMT

←Older revision		Revision as of 23:36, 8 March 2022
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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.		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.

-	Yellow-colored are the twelve 5-chain pentamers representing the 12 vertices that define the 20 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.	+	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.

	{{Clear}}		{{Clear}}

Eric Martz at 23:36, 8 March 2022

Eric Martz — Tue, 08 Mar 2022 23:36:02 GMT

←Older revision		Revision as of 23:36, 8 March 2022
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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.		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.

-	Yellow-colored are the 5-chain pentamers representing the 12 vertices that define the 20 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.	+	Yellow-colored are the twelve 5-chain pentamers representing the 12 vertices that define the 20 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.

	{{Clear}}		{{Clear}}

Eric Martz at 23:35, 8 March 2022

Eric Martz — Tue, 08 Mar 2022 23:35:26 GMT

←Older revision		Revision as of 23:35, 8 March 2022
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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.		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.

-	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.	+	Yellow-colored are the 5-chain pentamers representing the 12 vertices that define the 20 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.

	{{Clear}}		{{Clear}}

Eric Martz at 23:32, 8 March 2022

Eric Martz — Tue, 08 Mar 2022 23:32:46 GMT

←Older revision		Revision as of 23:32, 8 March 2022
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	This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in [[1sva]].		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 ~~triangular~~ 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 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<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.		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.

Eric Martz at 23:30, 8 March 2022

Eric Martz — Tue, 08 Mar 2022 23:30:44 GMT

←Older revision		Revision as of 23:30, 8 March 2022
Line 8:		Line 8:
	This model is based on the crystallographic solution of the VP1 capsid protein of Simian Virus 40, published in [[1sva]].		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.	+	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 triangular 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<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.		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.

Eric Martz at 17:19, 20 March 2017

Eric Martz — Mon, 20 Mar 2017 17:19:16 GMT

←Older revision		Revision as of 17:19, 20 March 2017
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	<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' />		<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> (capsid only)	+	*<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>

Eric Martz at 17:17, 20 March 2017

Eric Martz — Mon, 20 Mar 2017 17:17:41 GMT

←Older revision		Revision as of 17:17, 20 March 2017
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	<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' />		<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> (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>

Eric Martz at 12:24, 19 April 2010

Eric Martz — Mon, 19 Apr 2010 12:24:41 GMT

←Older revision		Revision as of 12:24, 19 April 2010
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<ref>Since each original chain 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.	+	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.

-	~~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.	+	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.

	{{Clear}}		{{Clear}}

Eric Martz at 12:22, 19 April 2010

Eric Martz — Mon, 19 Apr 2010 12:22:22 GMT

←Older revision		Revision as of 12:22, 19 April 2010
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 [[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 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.

	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.
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	==Content Attribution==		==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]].		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]].
		+
		+	==Notes==
		+	<references />

	==See Also==		==See Also==

Eric Martz at 10:16, 18 April 2010

Eric Martz — Sun, 18 Apr 2010 10:16:41 GMT

←Older revision		Revision as of 10:16, 18 April 2010
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	<!--		<!--
	* 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 [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]].		* The atomic coordinate file [[Image:1sva-cao.mmol.gz]].
		+	-->