1. Introduction to Virus Structure
Tutorial
Jonathan King, Peter Weigele, Greg Pintilie, David Gossard (MIT)
v.November, 2008

2. Virus Structure Size Basic shape Protective Shell - Capsid
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

3. 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

4. Electron Microscopy
Mitra, K. & Frank, J., Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annual review of biophysics and biomolecular structure, 35,

5. 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

6. 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

7. 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

8. Similarity to Buckminster Fuller’s Geodesic Domes

9. Icosahedral Symmetry 12 vertices 20 faces 5-3-2 symmetry axes
(equilateral triangles)
5-3-2 symmetry axes
60 identical* subunits
in identical environments
can form icosahedral shell
* asymmetric

10. Caspar and Klug’s Icosahedral shell

11. 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?

12. 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

13. 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

14. Spherical viruses have icosahedral symmetry

15. Homunculattice

16. HK97 Asymmetric Unit
Outside
Inside

17. Herpes Simplex Virus at 8.5 Å resolution
from Wah Chiu and Frazer Rixon in Virus Research (2002)

18. 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.

19. Influenza virus
composition of virus
entry of influenza
into cell

20. Influenza hemagglutinin:
a pH induced, conformationally controlled trigger
for membrane fusion
100 Å displacement
of fusion peptide
disordered loop
backbone is
structured
low pH
fusion peptide
Qiao et al. Membrane Fusion Activity of Influenza Hemagglutinin. The Journal of Cell Biology, Volume 141, 1998

21. Influenza Hemagglutinin
The HA spikes extend like a spring during infection

22. Trimer Structure Long alpha helices form coiled coil structure
In mature trimers of HA0, each monomer is cleaved into HA1 and HA2.

23. 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.

24. 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

26. P22 Pathway

28. Herpes viruses also have a portal protein
complex
Herpes portal (UL6) tagged with gold-bead labeled antibodies
visualized by negative stain electron microscopy
Bill Newcomb and Jay Brown, University of Virginia

29. Cryo-EM structure of purified Herpes portal protein
Trus BL, Cheng N, Newcomb WW, Homa FL, Brown JC, Steven AC. Structure and polymorphism of the UL6 portal protein of herpes simplex virus type 1. J Virol Nov;78(22):