FirstGlance/Virus Capsids and Other Large Assemblies: Difference between revisions
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==Polio Virus== | ==Polio Virus== | ||
Polio virus is small (among viruses pathogenic for humans) with an RNA genome inside a single-shell protein capsid. [[1pov]] | {{Template:ClickGreenLinks}} | ||
<jmol> | |||
The polio (poliomyelitis) virus mostly infects children under 5, and 1/200 infections causes permanent paralysis with 5-10% of those being fatal<ref name="polio-who">[https://www.who.int/news-room/fact-sheets/detail/poliomyelitis Poliomyelitis Overview, World Health Organization].</ref>. Vaccines were developed in the 1950s<ref name="polio-vaccines">[https://en.wikipedia.org/wiki/Polio#Vaccine Polio Vaccines at Wikipedia].</ref>. Polio is nearly eradicated worldwide, but endemic pockets persist in regions of Afghanistan and Pakistan where vaccination campaigns are most challenging<ref name="polio-eradication">[https://en.wikipedia.org/wiki/Polio#Eradication Eradication of Polio in Wikipedia].</ref><ref name="polio-who" />. Polio was declared eradicated from the Americas in 1994, but in 2022 a live vaccine-derived strain of polio was found circulating in parts of New York State, USA<ref name="polio-usa">[https://en.wikipedia.org/wiki/Polio#Americas Polio in the Americas, Wikipedia].</ref>. Polio vaccination is urged for all children, and for unvaccinated adults<ref name="polio-vaccschedule">[https://www.cdc.gov/vaccines/schedules/hcp/imz/child-adolescent.html Vaccination Schedule, US Centers for Disease Control and Prevention].</ref>. | |||
Polio virus is small (among viruses pathogenic for humans) with an RNA genome inside a single-shell protein capsid. [[1pov]] <jmol> | |||
<jmolLink> | <jmolLink> | ||
<script> | <script> | ||
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<text>captures an empty polio capsid</text> | <text>captures an empty polio capsid</text> | ||
</jmolLink> | </jmolLink> | ||
</jmol> | </jmol> made up from 3 proteins, 60 copies of each of '''VP0, VP1 and VP3''' (from proteolysis of polyprotein [https://www.uniprot.org/uniprotkb/P03300/entry UniProt P03300])<ref>PMID: 28811473</ref>. [[1pov]] provides the structure of the 3 chains in the [[asymmetric unit]], along with instructions for constructing the capsid ([[Biological Unit]] 1)<ref>PMID: 7849583</ref>. | ||
made up from 3 proteins, 60 copies of each of '''VP0, VP1 and VP3''' (from proteolysis of polyprotein [https://www.uniprot.org/uniprotkb/P03300/entry UniProt P03300])<ref>PMID: 28811473</ref>. [[1pov]] provides the structure of the 3 chains in the [[asymmetric unit]], along with instructions for constructing the capsid ([[Biological Unit]] 1)<ref>PMID: 7849583</ref>. | |||
The polio capsid has an icosahedral construction with 12 vertices defining 20 triangular faces. Notice that the larger blue mesas protruding on the surface have 5-fold symmetry. These are pentagonal capsomeres at the 12 vertices. The capsid is composed of 180 protein chains totaling about 377K non-H atoms. | The polio capsid has an icosahedral construction with 12 vertices defining 20 triangular faces. Notice that the larger blue mesas protruding on the surface have 5-fold symmetry. These are pentagonal capsomeres at the 12 vertices. The capsid is composed of 180 protein chains totaling about 377K non-H atoms. The molecular mass of this capsid structure is 5.9 MDa. | ||
'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=1pov polio virus capsid 1pov in FirstGlance] | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=1pov polio virus capsid 1pov in FirstGlance] | ||
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spin on; | spin on; | ||
</script> | </script> | ||
<text>all 60 copies of VP0 are isolated | <text>all 60 copies of VP0 are isolated</text> | ||
</jmolLink> | </jmolLink> | ||
</jmol> | </jmol> (shown as a half-capsid). | ||
Similarly one can easily isolate | Similarly one can easily isolate | ||
<jmol> | <jmol> | ||
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</jmolLink> | </jmolLink> | ||
</jmol> | </jmol> | ||
===Polio Resources=== | |||
* [[Art:Polio:_A_resolution_to_eradicate|Polio:_A_resolution_to_eradicate]] and the list of resources at the bottom of that page under [[Art:Polio:_A_resolution_to_eradicate#See_Also|See Also]]. | |||
==Eastern Equine Encephalitis Virus== | ==Eastern Equine Encephalitis Virus== | ||
{{Template: | {{Template:ClickGreenLinks}} | ||
'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 EEEV capsid 6mx4 in FirstGlance] | Human Eastern Equine Encephalitis is rare, with only a few cases reported in the USA each year. However, 30% of patients die, and there is no vaccine for humans and no specific medication. Many survivors have ongoing neurologic problems. The virus is spread by the bites of mosquitos that fed on infected animals.<ref name="eeev-cdc">[https://www.cdc.gov/easternequineencephalitis/index.html Eastern Equine Encephalitis Virus overview at the US Centers for Disease Control and Prevention].</ref><ref name="eeev-wp">[https://en.wikipedia.org/wiki/Eastern_equine_encephalitis Eastern Equine Encephalitis Virus article in Wikipedia].</ref> | ||
Eastern Equine Encephalitis Virus is an alphavirus with a single-stranded RNA genome enclosed in an icosahedral protein capsid that includes a lipid bilayer envelope<ref name="alphavirus">[https://en.wikipedia.org/wiki/Alphavirus Alphavirus article in Wikipedia].</ref>. {{Template:EEEV}} | |||
'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 EEEV capsid 6mx4 in FirstGlance] -- To cut away half of the capsid, depress the Slab button (in the Views tab). Then check both "Don't hide the back" and "Rotate slab". | |||
===Double-Shelled Capsid=== | ===Double-Shelled Capsid=== | ||
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{{Clear}} | {{Clear}} | ||
<br clear="both"> | |||
==Clathrin Coat== | ==Clathrin Coat== | ||
This <jmol> | This <jmol> | ||
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==Bacterial Gas Vesicle== | ==Bacterial Gas Vesicle== | ||
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"Gas vesicles allow a diverse group of bacteria and archaea to move in the water column by controlling their buoyancy. These gas-filled cellular nanocompartments are formed by up to micrometers long protein shells that are permeable only to gas."<ref name="gv">2022 Preprint: Cryo-EM structure of gas vesicles for buoyancy-controlled motility, by Stefan T. Huber, Dion Terwiel, Wiel H. Evers, David Maresca, and Arjen J. Jakobi. DOI [https://doi.org/10.1101/2022.05.08.489936 10.1101/2022.05.08.489936].</ref> <jmol> | "Gas vesicles allow a diverse group of bacteria and archaea to move in the water column by controlling their buoyancy. These gas-filled cellular nanocompartments are formed by up to micrometers long protein shells that are permeable only to gas."<ref name="gv">2022 Preprint: Cryo-EM structure of gas vesicles for buoyancy-controlled motility, by Stefan T. Huber, Dion Terwiel, Wiel H. Evers, David Maresca, and Arjen J. Jakobi. DOI [https://doi.org/10.1101/2022.05.08.489936 10.1101/2022.05.08.489936].</ref> <jmol> | ||
<jmolLink> | <jmolLink> | ||