FirstGlance/Virus Capsids and Other Large Assemblies: Difference between revisions

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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.


'''Quick Start''': [http://bioinformatics.org/firstglance/fgij4/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]


===Measuring Capsid Diameter===
===Measuring Capsid Diameter===
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{{Template:EEEV}}
{{Template:EEEV}}


'''Quick Start''': [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 EEEV capsid 6mx4 in FirstGlance]
'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 EEEV capsid 6mx4 in FirstGlance]


===Double-Shelled Capsid===
===Double-Shelled Capsid===
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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''': [https://bioinformatics.org/firstglance/fgij4/fg.htm?mol=3iyv Clathrin Coat 3iyv in FirstGlance]
'''Quick Start''': [https://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''': [https://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6bp8 Vault 6bp8 in FirstGlance]
'''Quick Start''': [https://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''': [https://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6bp8_consurf_APD0.56.pdb Vault with Conservation in FirstGlance] (all 61K alpha carbons)
'''Quick Start''': [https://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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</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 &mu;m 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 &mu;m in length with masses of hundreds of MDa<ref name="gv" />.


'''Quick Start''': [https://bioinformatics.org/firstglance/fgij4/fg.htm?mol=7r1c&bu=3 Gas Vesicle 7r1c in FirstGlance]
'''Quick Start''': [https://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://bioinformatics.org/firstglance/fgij4/fg.htm?mol=7r1c_N_consurf_APD0.59.pdb&bu=3 Evolutionary conservation of the gas vesicle in FirstGlance].
'''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>

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Karsten Theis
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