FirstGlance/How To Measure A Virus Capsid

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<StructureSection load='' size='350' side='right' caption='' scene=''>
<StructureSection load='' size='350' side='right' caption='' scene=''>
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<table style="background-color:#ffffa0;" class='wikitable'><tr><td>
 
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This page describes the use of FirstGlance in Jmol version 4.0. Its release is expected soon, but it is not yet publicly available. [[User:Eric Martz|Eric Martz]] 22:25, 26 July 2022 (UTC)
 
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</td></tr></table>
 
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{{Template:EEEV}}
{{Template:EEEV}}
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Quick Start: [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].
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'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].
[[FirstGlance in Jmol]] automatically constructs the capsid, and simplifies it to a subset of alpha carbon atoms small enough (not more than 25,000) to be analyzed efficiently in FirstGlance and [[JSmol]], both of which run in the Javascript of the web browser. FirstGlance offers a number of useful color schemes, including distance from center, colors that distinguish sequence-identical groups of chains, and [[Help:Color_Keys#Rainbows:_N_to_C.2C_5.27_to_3.27|amino-to-carboxy rainbow]]. When the structure is small enough that all alpha carbons can be displayed (not more than 250,000 alpha carbons; EEEV has 242,340), it can also be colored by charge, hydrophobic vs. polar, or [[evolutionary conservation]].
[[FirstGlance in Jmol]] automatically constructs the capsid, and simplifies it to a subset of alpha carbon atoms small enough (not more than 25,000) to be analyzed efficiently in FirstGlance and [[JSmol]], both of which run in the Javascript of the web browser. FirstGlance offers a number of useful color schemes, including distance from center, colors that distinguish sequence-identical groups of chains, and [[Help:Color_Keys#Rainbows:_N_to_C.2C_5.27_to_3.27|amino-to-carboxy rainbow]]. When the structure is small enough that all alpha carbons can be displayed (not more than 250,000 alpha carbons; EEEV has 242,340), it can also be colored by charge, hydrophobic vs. polar, or [[evolutionary conservation]].
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==Slab of the Capsid==
==Slab of the Capsid==
In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
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<jmol>
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{{Template:EEEV-slab}}
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<jmolLink>
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<script>
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script /wiki/images/e/ee/Echo-loading.spt;
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script /wiki/images/9/9f/6mx4-nohet-slab-distance.spt;
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spin on;
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</script>
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<text>Here is a slab of the center of the capsid.</text>
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</jmolLink>
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</jmol>
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Immediately you can see that this is a double-layered capsid, with outer and inner shells. Between the shells are transmembrane alpha helical "spikes" or "posts" embedded in a lipid bilayer (not represented by any atoms here).
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To obtain this slab in FirstGlance, you simply depress a ''Slab'' button. By default, the thickness of the slab is 10% of the diameter of the capsid (but this is adjustable). Here is a '''snapshot of the ''Views'' tab of FirstGlance'''. After the initial view of the capsid appears, getting this slab takes 3 clicks indicated by the red arrows: Click on the ''Views'' tab, depress the ''Slab'' button, and check ''Rotate slab''.
To obtain this slab in FirstGlance, you simply depress a ''Slab'' button. By default, the thickness of the slab is 10% of the diameter of the capsid (but this is adjustable). Here is a '''snapshot of the ''Views'' tab of FirstGlance'''. After the initial view of the capsid appears, getting this slab takes 3 clicks indicated by the red arrows: Click on the ''Views'' tab, depress the ''Slab'' button, and check ''Rotate slab''.
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</jmol>
</jmol>
(total 720 protein chains).
(total 720 protein chains).
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For more about the EEEV capsid, see [[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies#Eastern_Equine_Encephalitis_Virus|Virus Capsids and Other Large Assemblies]].
</StructureSection>
</StructureSection>
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==Reference==
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<references />

Current revision

Drag the structure with the mouse to rotate

Reference

  1. ↑ Hasan SS, Sun C, Kim AS, Watanabe Y, Chen CL, Klose T, Buda G, Crispin M, Diamond MS, Klimstra WB, Rossmann MG. Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Cell Rep. 2018 Dec 11;25(11):3136-3147.e5. doi: 10.1016/j.celrep.2018.11.067. PMID:30540945 doi:http://dx.doi.org/10.1016/j.celrep.2018.11.067

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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