1/26/09 VIRUS STRUCTURESergei Nekhai, Ph.D.

Objectives:

•Functional organization of viral particles

• Viral Symmetry

• Viral Capsids

•Viral Envelope

Viruses

Figure 13.1

Structure of Viruses• Size range –

– most <0.2 μm; requires electron microscope• Virion – fully formed virus able to establish

an infection

Organization of Viral Particles

•Contains RNA or DNA

•Form a protective package

•Transmit genetic material

•Entry, multiply and exit the host•Redirect cellular machinery

E. coli Streptococcus

Yeast Cell

From Medical Microbiology, 5th ed., Murray, Rosenthal & Pfaller, Mosby Inc., 2005, Fig. 6-4.

Viral Particles: Sizes, masses and dimensions

Viruses:•Weights: 3-800 X 106 Da • 25 - 100 nm diameter

Bacteria:≈1500 nm diameter

Eukaryotic cells :≈20,000 nM diameter

Viruses - Structure

• contain DNA or RNA

• contain a protein coat (capsid)

• Some are enclosed by an envelope

• Some viruses have spikes

Terminology• Capsid (syn: coat): regular, shell-like structure composed of

aggregated protein subunits which surrounds the viral nucleic acid•• Nucleocapsid (syn: core): viral nucleic acid enclosed by a capsid

protein coat

• Envelope (syn: viral membrane): lipid bylayer containing viral glycoproteins. The phospholipids in the bylayer are derived from the cell that the virus arose from. Not all viruses have envelopes some consist of only the nucleocapsid

• Virion: physical virus particle. Nucleocapsid alone for some viruses (picornaviruses) or including outer envelope structure for others (retroviruses).

Virion

Figure 13.5a

• A virion is a complete, fully developed viral particle– Obligate intracellular parasite– Lack many of the features of living things– Vehicle of transmission from one host to another– A major cause of disease

General Structure of Viruses• Capsids

– All viruses have capsids - protein coats that enclose and protect their nucleic acid.

– Each capsid is constructed from identical subunits called capsomers made of protein.

– The capsid together with the nucleic acid are nucleoscapsid.

– Some viruses have an external covering called envelope; those lacking an envelope are naked

ComponentsComponents

• GENOME

• CAPSID

• CAPSOMERES

• ENVELOPE

• SPIKES

• ENZYMES

The Viral Capsid• Capsid- Protein coat that encapsidates the viral genome.• Nucleocapsid-Capsid with genome inside (plus anything

else that may be inside like enzymes and other viral proteins for some viruses).

Capsid functions1. Protect genome from atmosphere (May include damaging

UV-light, shearing forces, nucleases either leaked or secreted by cells).

2. Virus-attachment protein- interacts with cellular receptor to initiate infection. Since viruses are made of many different repeated subunits thereis redundancy; Many receptor sites so damage to a few doesn’t prevent infection.

3. Delivery of genome in infectious form. May simply “dump” genome into cytoplasm (most +ssRNA viruses) or serve as the core for replication (retroviruses and rotaviruses).

Human Viruses

"Group" Family Genome Genome size (kb) Capsid EnvelopedsDNA

Poxviridae dsDNA, linear 130 to 375 Ovoid YesHerpesviridae dsDNA, linear 125 to 240 Icosahedral YesAdenoviridae dsDNA, linear 26 to 45 Icosahedral NoPolyomaviridae dsDNA, circular 5 Icosahedral NoPapillomaviridae dsDNA, circular 7 to 8 Icosahedral No

ssDNAAnellovirus ssDNA circular 3 to 4 Isometric NoParvoviradae ssDNA, linear, (- or +/-) 5 Icosahedral No

RetroHepadnaviridae dsDNA (partial), circular 3 to 4 Icosahedral YesRetroviridae ssRNA (+), diploid 7 to 13 Spherical, rod or cone shaped Yes

dsRNAReoviridae dsRNA, segmented 19 to 32 Icosahedral No

ssRNA (-)Rhabdoviridae ssRNA (-) 11 to 15 Helical YesFiloviridae ssRNA (-) 19 Helical YesParamyxoviridae ssRNA (-) 10 to 15 Helical YesOrthomyxoviridae ssRNA (-), segmented 10 to 13.6 Helical YesBunyaviridae ssRNA (-, ambi), segmented 11 to 19 Helical YesArenaviridae ssRNA (-, ambi), segmented 11 Circular, nucleosomal YesDeltavirus ssRNA (-) circular 2 Spherical Yes

ssRNA (+)Picornaviridae ssRNA (+) 7 to 9 Icosahedral NoCalciviridae ssRNA (+) 7 to 8 Icosahedral NoHepevirus ssRNA (+) 7 Icosahedral NoAstroviridae ssRNA (+) 6 to 7 Isometric NoCoronaviridae ssRNA (+) 28 to 31 Helical YesFlaviviridae ssRNA (+) 10 to 12 Spherical YesTogaviridae ssRNA (+) 11 to 12 Icosahedral Yes

Principles of Viral Architecture•Viral capsid are made of repated protein subunits

•Capsids are self assembled•Fraenkel-Conrat and Williams (1955): self-assembly of TMV

•Proteins and nucleic acids are held together with non-covalent bonds

•Protein-protein, protein-nucleic acid, protein-lipid

•Helical or icosahedral symmetry

Viral Capsids• If If 1 protein for 1 capsid:

– Need > 18,000 amino acids.– Need > 54,000 nucleotides.– Small viruses hold max. of 5,000 nucleotides.

• Must use many copies of 1 (or a few) protein(s).• High symmetry

– Minimizes # different subunit interactions involved with assembly.

– Simpler protein.– Self assembly:

• Self-contained assembly "instructions".

Basic Nucleocapsid Structures:

• HELICAL: Rod shaped, varying widths and specific architectures; no theoretical limit to the amount of nucleic acid that can be packaged

• CUBIC (Icosahedral): Spherical, amount of nucleic acid that can be packaged is limited by the of the particle

• Irregular: Without clear symmetry

Capsid and EnvelopeNon-enveloped

Icosahedral Enveloped

Helical

Capsid:•Protect viral nucleic acid•Interact with the nucleic acid for packaging•Interact with vector for specific transmission •Interact with host receptors for entry to cell and to release of nucleic acid

Envelope:•Made from host cell membrane (plasma, ER or Golgi)•Fuse for Entry

Helical viruses• Probably evolved along with other helical structures like

DNA, α-helix, etc.• Allow flexibility (bending) • Helical viruses form a closely related spring like helix

instead. The best studied TMV but many animal viruses and phage use this general arrangement. – Note-all animal viruses that are helical are enveloped, unlike many of

the phage and plant viruses. • Most helixes are formed by a single major protein arranged

with a constant relationship to each other (amplitude and pitch).

• They can be described by their Pitch (P, in nm):• P= m x p, m-# of protein subunits per helical turn, p-axial rise

per subunit

Helical symmetry• Tobacco mosaic virus is typical,

well-studied example• Each particle contains only a single

molecule of RNA (6395 nucleotide residues) and 2130 copies of the coat protein subunit (158 amino acid residues; 17.3 kilodaltons)– 3 nt/subunit– 16.33 subunits/turn– 49 subunits/3 turns

• TMV protein subunits + nucleic acid will self-assemble in vitro in an energy-independent fashion

• Self-assembly also occurs in the absence of RNA

TMV rod is 18 nanometers (nm) X 300 nm

The Structure of an Influenza virus

Envelope Spikes Helical nucleoprotein

Vesicular Stomatitis Virus• VSV coat protein (50 aa): alpha helical with 3 distinct domains:

+ charge interacts with nucleic acid, hydrophobic with proteins on either side, negative charge with polar environment

• Subunits are tilted 20o relative to the long axis of the particle. • VSV Genome: 11,000 nt -ssRNA interacts with the nucleocapsid

protein (N) to form a helical structure with P=5 nm. •

Structure of Animal Viruses

ICOSAHEDRAL VIRUSES

•1956, Watson and Crick – only cubic symmetry leads to isometric particle•Only three cubic symmetry exist:

•tetrahedral (2:3) – 12 identical subunits •octahedral (4:3:2) – 24 identical subunits •icosahedral (5:3:2) – 60 identical subunits

•For viruses of 150-200 Å - ~ 60 of 20 kDa protein subunits

•However, for viruses > 250 Å (turnip yellow mosaic), it was more than 60 subunits

Non-enveloped virus• The nucleic acid of a virus is surrounded by a capsid.• Each capsid is composed of protein subunits called

capsomeres.

QUASI-EQUIVALENCE1962, Caspar and Klug – found a principal of building

icosahedral structures from similar blocks

• Shell is built from the same blocks•Bonds are deformed in a slightly different ways•Assumed a possibility of 5 degrees deformation•Shell can contain 60n subunits

A Fuller godesic domeThat inspired Caspar and Klug

Triangulation number (T) Enumerated by Caspar and Klug

• T=f2 x P where f=# of subdivisions on each side of a triangular face, P=h2 + hk + k2 where h and k are any nonnegative integer

• Only T’s that may be derived from the above equation are possible.

• 60 = minimal number of irregular subunits required

CLASSES OF ICOSAHEDRAL DELTAHEDRA

Tabulation of the Triangulation Number T

Class

P = 1 1 4 9 16 25 . . . .

P = 3 3 12 27 . . . .

Skew Classes 7 13 19 21 . . . .

T = Pf2, where P = h 2 + hk + k 2, h and k any pair of integers with no common factor, and f= 1 , 2 , 3 , 4 , . . . .

Number morphological units M = 10 T + 2= 10(T-1) hexamers + 12 pentamers

(a) P=1, T=1. (b) P = 1, T= 4. (c) and (d), P = 3 (T=3 and 12, respectively). (e), (f), (g) and (h), first members of the skew classes P = 7, 13, 19, and 21, respectively.

CLASSES OF ICOSAHEDRAL DELTAHEDRA

Different Aarrangements of Icosahedral Symmetry

Zlotnick A. PNAS 2004;101:15549-15550

©2004 by National Academy of Sciences

Jellyroll: Many, but not all Viral proteins

Capsid proteins

β-barrel.• Rhombohedral wedges:

– Fit into icosahedron.• Jellyroll topology• Conserved in many small

viruses– T = 1, 3, …

• 60, 180, 240 proteins…– RNA or DNA viruses.

• Essentially no sequence homology.

Picornaviridae, a prototype T=3 virus• Quasi-equivalence with pentamer at each vertex

and hexamers in other regions; • Triangulation # = 3. • Note that VP-4 is not on the surface of the

structure but lies under the face.

Picornaviridae, a prototype T=3 virus• The protein subunits that form each protomer all assume a similar

(not identical) shape .• In fact all T=3 RNA viruses have proteins that form “8 strand

antiparallel b barrels”. • The structures form from the polypeptide by first forming a “jelly-roll

barrel” that then goes on to form the wedge-shaped barrel when the capsid is being formed.

• Each particle contains only a single molecule of RNA (4800 nt) and 180 copies of the coat protein subunit (387 aa; 41 kd)

• Viruses similar to TBSV will self-assemble in vitro from protein subunits + nucleic acid in an energy-independent fashion

TBSV icosahedron is 35.4 nm in diameter

Protein Subunits Capsomeres

T= 3 LatticeC

N

Tomato Bushy Stunt Virus

The Structure of a Herpesvirus

Spikes EnvelopeIcosahedral cores

Tegument

Enveloped viruses• In an enveloped virus, the capsid is covered by an

envelope – The envelope is usually made of some combination of lipids,

proteins, and carbohydrates– Some envelopes contains spikes that allow them to attach to the

host

Enveloped virusesEnveloped viruses

• Envelope lipids are host cell-derived. Envelope proteins are virus-encoded

• Envelope proteins are important for host cell recognition and penetration