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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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{{Template:EEEV}}
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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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'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].
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</td></tr></table>
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[[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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The
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==Slab of the Capsid==
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In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
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{{Template:EEEV-slab}}
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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''.
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[[Image:Firstglance-slab-controls.png]]
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==Measuring the Slab==
<jmol>
<jmol>
<jmolLink>
<jmolLink>
<script>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/e/ee/Echo-loading.spt;
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script /wiki/images/5/56/6mx4-capsid-nohet-distance.spt;
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script /wiki/images/5/52/6mx4-nohet-slab-distance-diameters2.spt;
spin on;
spin on;
</script>
</script>
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<text>capsid of Eastern Equine Encephalitis Virus</text>
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<text>The outside diameter of the capsid is about 644 Angstroms.</text>
</jmolLink>
</jmolLink>
</jmol>
</jmol>
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(EEEV) consists of three distinct protein sequences, and a total of 720 chains. It has nearly 2 million non-hydrogen atoms (so about 3.6 million atoms including hydrogen). The structure [[6mx4]] determined by electron microscopy (4.4 &Aring; resolution) has 12 chains, with instructions for constructing the entire capsid using 60 copies of the asymmetric unit.
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In FirstGlance (and JSmol), distances are measured by double-clicking on first one, then the second of the two relevant atoms. The distance between the centers of two of the outermost blue atoms is '''644 &Aring;''', while the distance between two of the innermost red atoms is '''315 &Aring;'''. The length of the transmembrane spikes/posts is about '''35 &Aring;''', consistent with the thickness of a lipid bilayer.
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[[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 the 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 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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==Three Protein Sequences==
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==Slab of the Capsid==
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In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
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<jmol>
<jmol>
<jmolLink>
<jmolLink>
<script>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
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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script /wiki/images/2/26/6mx4-nohet-slab-seqid.spt;
spin on;
spin on;
</script>
</script>
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<text>Here is a slab of the center of the capsid.</text>
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<text>The capsid is made up of 240 copies of each of 3 protein sequences
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</text>
</jmolLink>
</jmolLink>
</jmol>
</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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(total 720 protein chains).
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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''.
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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]].
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[[Image:Firstglance-slab-controls.png]]
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</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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