FirstGlance/Virus Capsids and Other Large Assemblies: Difference between revisions
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<StructureSection load='' size='350' side='right' caption='' scene='91/918450/1pov/2'> | <StructureSection load='' size='350' side='right' caption='' scene='91/918450/1pov/2'> | ||
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This page describes the use of version 4.0 of FirstGlance in Jmol. Its release is expected soon, but it is not yet publicly available. You can test [http://bioinformatics.org/firstglance/fgij4/ this near-final version] which is also used in the ''FirstGlance'' links below, but if you upload a file it will revert to the older version of FirstGlance. | This page describes the use of version 4.0 of FirstGlance in Jmol. Its release is expected soon, but it is not yet publicly available. You can test [http://bioinformatics.org/firstglance/fgij4/ this near-final version] which is also used in the ''FirstGlance'' links below, but if you upload a file it will revert to the older version of FirstGlance. | ||
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Virus capsids and similarly large protein assemblies can be conveniently visualized and analyzed with [[FirstGlance in Jmol]]. Below some examples are explained and illustrated, but here is a '''quick start''': [http:// | Virus capsids and similarly large protein assemblies can be conveniently visualized and analyzed with [[FirstGlance in Jmol]]. Below some examples are explained and illustrated, but here is a '''quick start''': [http://firstglance.jmol.org/fg.htm?mol=1pov polio virus capsid in FirstGlance] ([[1pov]]). | ||
FirstGlance in Jmol automatically constructs [[biological unit]] 1, thought to be the major functional quaternary assembly. [http:// | FirstGlance in Jmol automatically constructs [[biological unit]] 1, thought to be the major functional quaternary assembly. [http://firstglance.jmol.org/notes.htm#bu Biological unit 1 is shown initially by default], and you can start separate sessions to show the [[asymmetric unit]] or other biological units when more than one are specified. When the resulting assembly is too large to work smoothly and efficiently in FirstGlance in Jmol (all Javascript), FirstGlance will [http://firstglance.jmol.org/notes.htm#simplification automatically simplify the model] to alpha carbons, or when necessary, to a subset of alpha carbons. | ||
Most of the scenes below use color schemes that are built into FirstGlance, and are displayed very easily with just a few clicks of the mouse. The evolutionary conservation color scheme requires that the model be pre-processed by the [[ConSurf/Index|ConSurf Server]]. It produces a PDB file understood by FirstGlance, which will automatically color the model by evolutionary conservation in its initial view. | Most of the scenes below use color schemes that are built into FirstGlance, and are displayed very easily with just a few clicks of the mouse. The evolutionary conservation color scheme requires that the model be pre-processed by the [[ConSurf/Index|ConSurf Server]]. It produces a PDB file understood by FirstGlance, which will automatically color the model by evolutionary conservation in its initial view. | ||
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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:// | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=1pov polio virus capsid 1pov in FirstGlance] | ||
===Measuring Capsid Diameter=== | ===Measuring Capsid Diameter=== | ||
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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:// | 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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</jmol>, each modeled as 70 of 243 residues of [https://www.uniprot.org/uniprotkb/P04973/entry UniProt P04973]. | </jmol>, each modeled as 70 of 243 residues of [https://www.uniprot.org/uniprotkb/P04973/entry UniProt P04973]. | ||
'''Quick Start''': [ | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=3iyv Clathrin Coat 3iyv in FirstGlance] | ||
===Amino and Carboxy Termini=== | ===Amino and Carboxy Termini=== | ||
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This model has nearly one million atoms (including hydrogens), and 61K alpha carbons. | This model has nearly one million atoms (including hydrogens), and 61K alpha carbons. | ||
'''Quick Start''': [ | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6bp8 Vault 6bp8 in FirstGlance] | ||
===Evolutionary Conservation=== | ===Evolutionary Conservation=== | ||
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{{Template:ColorKey_ConSurf_NoYellow_NoGray}} | {{Template:ColorKey_ConSurf_NoYellow_NoGray}} | ||
'''Quick Start''': [ | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6bp8_consurf_APD0.56.pdb Vault with Conservation in FirstGlance] (all 61K alpha carbons) | ||
Conservation analysis was performed by [[ConSurf/Index|ConSurf]]. In order for the pattern to be meaningful, all 61K alpha carbons were loaded into FirstGlance, which then applied the conservation colors. | Conservation analysis was performed by [[ConSurf/Index|ConSurf]]. In order for the pattern to be meaningful, all 61K alpha carbons were loaded into FirstGlance, which then applied the conservation colors. | ||
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==Bacterial Gas Vesicle== | ==Bacterial Gas Vesicle== | ||
{{Template:ClickGreenLinks}} | |||
"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> | ||
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</jmol> ([[7r1c]]). The actual nanocompartments are much longer, and taper down to conical caps at the ends.<ref name="gv" /> Actual gas vesicles vary in diameter, with some being about twice the diameter of this model.<ref name="gv" /> This model has 930 copies of a single protein sequence of 88 amino acids (GVpA, [https://www.uniprot.org/uniprotkb/A0A0B6AAV2/entry UniProt A0A0B6AAV2]). It is 9 MDa with about 900K atoms including hydrogen and 60,450 alpha carbons. Actual gas vesicles can approach 1 μm in length with masses of hundreds of MDa<ref name="gv" />. | </jmol> ([[7r1c]]). The actual nanocompartments are much longer, and taper down to conical caps at the ends.<ref name="gv" /> Actual gas vesicles vary in diameter, with some being about twice the diameter of this model.<ref name="gv" /> This model has 930 copies of a single protein sequence of 88 amino acids (GVpA, [https://www.uniprot.org/uniprotkb/A0A0B6AAV2/entry UniProt A0A0B6AAV2]). It is 9 MDa with about 900K atoms including hydrogen and 60,450 alpha carbons. Actual gas vesicles can approach 1 μm in length with masses of hundreds of MDa<ref name="gv" />. | ||
'''Quick Start''': [ | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=7r1c&bu=3 Gas Vesicle 7r1c in FirstGlance] | ||
===Hydrophobic Inner Surface=== | ===Hydrophobic Inner Surface=== | ||
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{{Template:ColorKey_ConSurf_NoYellow_NoGray}} | {{Template:ColorKey_ConSurf_NoYellow_NoGray}} | ||
'''Quick Start''': [http:// | '''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=7r1c_N_consurf_APD0.59.pdb&bu=3 Evolutionary conservation of the gas vesicle in FirstGlance]. | ||
<jmol> | <jmol> | ||