Introduction to Virus Structure
TutorialJonathan King, Peter Weigele, Greg Pintilie, David Gossard
(MIT)
v.November, 2008
Virus Structure
• Size– 17 nm – 3000 nm diameter
• Basic shape– Rod-like– “Spherical”
• Protective Shell - Capsid– Made of many identical protein
subunits– Symmetrically organized– 50% of weight– Enveloped or non-enveloped
• Genomic material– DNA or RNA– Single- or double-stranded
Virus Structure
• Virus capsids function in: – Packaging and protecting nucleic acid– Host cell recognition
• Protein on coat or envelope “feels” or “recognizes” host cell receptors
– Genomic material delivery• Enveloped: cell fusion event• Non-enveloped: more complex strategies &
specialized structures
Electron Microscopy
Mitra, K. & Frank, J., 2006. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annual review of biophysics and biomolecular structure, 35, 299-317.
History
• In 1953, Crick & Watson proposed … principles of virus structure– Key insight:
• Limited volume of virion capsid => nucleic acid sufficient to code for only a few sorts of proteins of limited size
– Conclusion:• Identical subunits in identical environments• Icosahedral, dodecahedral symmetry
X-ray Crystallography of Viruses
• Symmetry of protein shells makes them uniquely well-suited to crystallographic methods
• Viruses are the largest assemblies of biological macromolecules whose structures have been determined at high resolution
History con’t
• In 50’s & 60’s Klug and others confirmed that several (unrelated) “spherical” viruses had icosahedral symmetry– (Used negative staining & electron microscopy)
• Conclusion:– Icosahedral symmetry is preferred in virus structure
Icosahedral Symmetry
• 12 vertices
• 20 faces(equilateral triangles)
• 5-3-2 symmetry axes
• 60 identical* subunits in identical environments can form icosahedral shell * asymmetric
But …• Clear evolutionary pressure to make larger capsid
– Using larger subunits helps very little– Using more subunits helps a lot
• Not possible to form icosahedral shell (of identical units in identical environments) with more than 60 subunits
• Viruses with more than 60 subunits were observed
• Question:– How can >60 subunits form an icosahedral shell?– Will any number of subunits work?– If so, how would they be organized?
Quasi-equivalence• In 1962, Caspar & Klug proposed the
theory of “quasi-equivalence”
– Not all protein subunits are equivalent• “Identical” subunits in slightly different
environments
– Only certain numbers of subunits will can be packed into closed regular lattice.
Caspar & Klug, Cold Spring Harbor, 1962
Quasi-equivalence
• Subunits are in “minimally” different environments– Pentamers at vertices
– Hexamers elsewhere
• Predicts packing arrangements of larger capsids– Shift from T1 to T4 packing
=> 8-fold increase in volume
Influenza
• Infection depends on spike proteins projecting from capsid membrane called “Hemagglutinin (HA)”
• These bind sugar molecules on cell surface
• Much of the difference between Hong Kong flu, Swine flu, Bird flu, and other strains, is in the amino acid sequence and conformation of the HA protein.
• These differences control what host cell types the virus can infect.
• Immunization against flu involves your immune system synthesizing antibody proteins that bind the HA protein.
low pH
100 Å displacementof fusion peptide
fusion peptide
Influenza hemagglutinin:a pH induced, conformationally controlled trigger
for membrane fusion
backbone isstructured
disordered loop
Qiao et al. Membrane Fusion Activity of Influenza Hemagglutinin. The Journal of Cell Biology, Volume 141, 1998
Influenza Hemagglutinin
• The HA spikes extend like a spring during infection
http://www.roche.com/pages/facets/10/viruse.htmhttp://hsc.virginia.edu/medicine/basic-sci/cellbio/jgruenke.html
Trimer Structure
• Long alpha helices form coiled coil structure
• In mature trimers of HA0, each monomer is cleaved into HA1 and HA2.
Evolution of dsDNA viruses
• All known viruses, whether infecting bacteria or humans, may have evolved from a single common ancestor, relatively early in the evolution of organisms.
Common steps in the assembly of all dsDNA viruses
• Unique portal ring at one Vertex
• Scaffolding proteins
• Procapsid assembled empty of DNA
• DNA pumped into procapsid through portal ring
• DNA moves back through portal to enter cell
Herpes viruses also have a portal protein
Herpes portal (UL6) tagged with gold-bead labeled antibodiesvisualized by negative stain electron microscopy
portalcomplex
Bill Newcomb and Jay Brown, University of Virginia