Lect. 6 composition & Architecture of plant viruses

Composition & Architecture 

of plant viruses 

P.N. Sharma 

Department of Plant Pathology, 

CSK HPKV, Palampur (H.P.)

Plant Viruses 

Classification, Morphology, Genome, 

and Structure

Importance 

• Detailed knowledge of virus structure is 

important to understand different aspects of 

virology e.g. how virus survive, infect, spread, 

replicate and how they are related with one 

other. 

• Knowledge of virus architecture has increased 

greatly with the invention of EM, optical 

defraction, X-ray crystallography procedures; 

• Molecular techniques 

• Chemical information about viruses

Morphology of Viruses 

• About ½ of all known plant viruses are 

elongate (flexuous threads or rigid rods). 

• About ½ of all known plant viruses are 

spherical (isometric or polyhedral). 

• A few viruses are cylindrical bacillus-like 

rods.

Chemical composition of plant viruses 

• Protein( Capsid) 

• Capsomere 

• Nucleic acids 

• RNA 

• +ve strand RNA 

• -ve strand RNA 

• ssRNA 

• dsRNA 

• DNA 

• ssDNA 

• dsDNA

Viral Composition 

• Proteins 

• 60-95% of the virion 

• Repeating subunits, identical for each virus type but 

varies from virus to virus and even from strain to 

strain 

• TMV subunits - 158 amino acids with a mass of 17,600 

Daltons (17.6 kDa, kd or K) 

• TYMV – 20,600 Dalton protein 

• Nucleic acid is 5-40% of the virion 

• Spherical viruses: 20-40% 

• Helical viruses: 5-6%

Viral Composition 

• Nucleic acid (5-40%) represents the genetic 

material, indispensable for replication 

• Nucleic acid alone is sufficient for virus 

replication – Fraenkel-Conrat, Schramm 

• Protein (60-95%) protects virus genome 

from 

• degradation 

• facilitates movement through the host and 

• transmission from one host to another

A/a composition of capsid proteins of some viruses 

1. Alanine 

CMV: 17; PVY: 16 

TMV: 14; PVX: 76 

2. Arginine 

CMV: 24; PVY: 11 

TMV: 11; PVX: 18 

3. Asparatic acid 

CMV: 30; PVY: 22 

TMV: 18; PVX: 42 

6. Glutamine 

CMV: 20; PVY: 23 

TMV: 16; PVX: 33 

11. Leucine 

CMV: 26; PVY: 10 

TMV: 12; PVX: 19 

7. Glutamic acid 12. Lysine 

CMV: 18; PVY: 13 

TMV: 2; PVX: 22 

8. Glycine 

CMV: 16; PVY: 13 

TMV: 6 ; PVX: 23 

4. Asparagines 9. histidine 

CMV: 4; PVY: 4 

TMV: - ; PVX: 4 

5. Cystein 


TMV: 1; PVX: 5 

10. Isoleucine 

CMV: 16; PVY: 12 

TMV: 9 ; PVX: 21 

13. Methionine 


TMV: 0 ; PVX: 15 

14. Phenylalanine 

CMV: 7 ; PVY: 5 

TMV: 8; PVX: 22 

15. Proline 

CMV: 18; PVY: 11 

TMV: 8 ; PVX: 34 

16. Serine 

CMV: 32; PVY: 10 

TMV: 16; PVX: 31 

17. Tryptophane 

CMV: 1 ; PVY: 2 


18. Tyrosine 

CMV: 11; PVY: 6 


19. Threonine 

CMV: 17; PVY: 13 

TMV: 16; PVX: 58 

20. Valine 

CMV: 22; PVY: 13 

TMV: 14; PVX: 27 

Total CMV: 287 PVY: 203 TMV: 158 PVX: 463

%age of protein & n/a in some viruses 

%age of protein & n/a in some viruses 

Virus n/a (%) Protein (%) 

TMV 5 95 

PVX 6 94 

PVY 5 95 

CpMV 31-33 67-69 

CMV 18 82 

TRSV 40 60

Viral Ultrastructure 

• Terminology for virus components 

• Capsid is the protein shell that encloses the 

nucleic acid 

• Capsomers are the morphological units seen 

on the surface of particles and represent 

clusters of structure units 

• Capsid and enclosed nucleic acid is called the 

nucleocapsid 

• The virion is the complete infectious virus 

particle 

Caspar, D. L. D. and Klug, A. (1963) "Structure and Assembly of Regular Virus Particles." In 

Viruses, Nucleic Acids, and Cancer, 17th Annual Symposium on Fundamental Cancer 

Research, University of Texas, Williams and Wilkins, Baltimore, pp. 27-39.

Watson and Crick 

• In 1956 proposed: 

• Amount of the virus nucleic acid was 

insufficient to code for more than a few 

proteins of limited size 

• Therefore the protein shell must be of identical 

subunits 

• Subunits had to be arranged to provide 

each with an identical environment, i.e., 

symmetrical packing

Virus Architecture 

• Detailed knowledge of virus structure is 

important to understand different aspects 

of virology 

• Knowledge of virus architecture has 

increased greatly with the innovation like 

EM, optical defraction, X-Ray 

crystallography procedures, mol. 

techniques and chemical nature of the 

virus.

Various feature of viruses can be 

estimated by studying: 

• Chemical & biochemical studies 

• Size of particles 

• Hydrodynamics 

• Laser scattering has been used to determine the 

radii of spherical viruses 

• E.M. 

• X-ray crystallography 

• it gives accurate estimates of radius of icosahedral 

viruses but condition is that the virus should be able to 

form stable crystals.

Electron microscopy 

• In 1924 L. de BROGLIE discovered the wave-character 

of electron rays thus giving the prerequisite for the 

construction of the electron microscope. 

• Invented by M. KNOLL and E. RUSKA (Technische 

Universität Berlin, 1932). 

• One of the first biological objects observed was the 

tobacco mosaic virus (TMV). 

• The first picture of a cell was published in 1945 by K. R. 

PORTER, A. CLAUDE and E. F. FULLAM (Rockefeller 

Institute, New York). 

• The Transmission Electron Microscope (TEM) 

• The Scanning electron microscope (SEM)

• The Transmission Electron Microscope (TEM)

• The Transmission Electron Microscope (TEM) 

A 1973 Siemens electron microscope, EM developed by E. Ruska 1933

Fine structures determination 

E.M. 

• Metal shadow preparations: using heavy 

metals, it enhances the contrast of particles 

• Freeze drying: useful about surface details 

particularly with lipid protein bilayer 

mambranes (Large viruses) 

• Negative staining: the use of electron dense 

stains is more important than heavy metals 

shadowing for morphological details. 

• Such stains may be +ve or –ve

• Positive stains 

• React chemically with and are bound to virus 

surface e.g. various Osmium, lead and uranyl 

compounds and phosphotungustic acid (PTA) are 

used under appropriate conditions. However, the 

chemical reaction may alter or disintegrate the virus 

so –ve stains are more important 

• Negative stains: 


• They do not react with the virus but penetrate 

available spaces on the surfaces or with in virus 

particle e.g. Uranylacetate or Potassium 

phosphotungstate (KPT) are used near pH 5.0


• Thin sections 

• Cryo EM 

• X-ray crystallography analysis 

• Neutron small angle scattering: 

• neutron scattering by virus solution is a method by which 

low resolution information can be obtained about 

structure of virus. E.g. important for radii of isometric 

particles 

• Mass spectrography 

• Serological method's 

• Gel diffusion 

• ELISA 

• ISEM

Methods for studying stabilizing 

bonds 

• The primary structure of viral CP & n/a depends 

upon covalent bonds. 

• Three kinds of interactions are involved in viruses 

: 

• Protein : protein 

• Protein : RNA 

• RNA : RNA 

These help the CP and n/a 

to be held together 

precisely 

• In addition, small molecules e.g. divalent metal 

ions (CA2+ in particular) have marked effects on 

the stability of some viruses. 

• These interactions determine 

• how much the virus is stable 

• How it might be assembled during virus synthesis 

• How viral n/a is released following infection of cell

Methods for studying stabilizing bonds 

• The stabilizing interactions are hydrophobic 

bonds, H= bonds, salt linkage etc. these 

interactions cab be studied by: 

• X-ray crystallography 

• Stability to chemicals and physical agents: e.g. 

Phenol, urea, temperature and detergents etc. 

• Chemical modification of CP: a/a changes 

• Removal of ions: in viruses whose structure are 

stabilized by Ca2+ ions can be affected by their 

removal e.g. in isometric particles, CA2+ ions 

removal by EDTA causes swelling of the particles. So 

this phenomenon can give information about the kind 

of bond important fro virus stability.

Methods for studying stabilizing bonds 

• Circular dichroism: Spectra can be used 

to obtain estimates of the extent of a- 

helix and B- structure in a viral protein 

subunit. 

• n/a tests

Architecture of rod shaped viruses 

• Crick & Watson (1956) put forwarded a 

hypothesis regarding structures of small viruses 

(TYMV & TMV) that: 

• Viral RNA enclosed in CP 

• Naked RNA is infectious 

• Basic requirement is protein shell to protect n/a etc. 

• In rod shaped viruses, the protein subunits are 

arranged in a helical manner regardless of protein 

subunit number into a helical array.

X-ray crystallography 

• X-ray crystallography is a method of determining the 

arrangement of atoms within a crystal, in which a 

beam of X-rays strikes a crystal and diffracts into 

many specific directions. 

• From the angles and intensities of these diffracted 

beams, a crystallographer can produce a threedimensional 

picture of the density of electrons within 

the crystal. 

• From this electron density we can determined: 

• the mean positions of the atoms in the crystal, as well as 

• their chemical bonds, 

• their disorder and various other information.

X-ray sources 

• The brightest and most 

useful X-ray sources 

are synchrotrons 

A protein crystal seen under amicroscope. 

Crystals used in X-ray crystallography may 

be smaller than a millimeter across. 

Workflow for solving the 

structure of a molecule by X- 

ray crystallography.

Diffractometer 

A Diffractometer is a measuring 

instrument for analyzing the structure of a 

material from the scattering pattern 

produced when a beam of radiation or 

particles (as X rays or neutrons) interacts 

with it. 

Principle 

• Because it is relatively easy to 

use electrons or neutrons having wavelengths smalle 

r than a nanometer, electrons and neutrons may be 

used to study crystal structure in a manner very 

similar to X-ray diffraction. Electrons do not penetrate 

as deeply into matter as X-rays, hence electron 

diffraction reveals structure near the surface; 

neutrons do penetrate easily and have an advantage 

that they possess an intrinsic magnetic moment that 

causes them to interact differently with atoms having 

different alignments of their magnetic moments. 

An X-ray diffraction pattern of a 

crystallized enzyme. The pattern o 

spots (called reflections) can be used to 

determine the structure of the enzyme.

TMV 

• TMV particles are: 

• Rigid helical rods 

• 300 nm long X 18 nm dia 

• 95% protein & ~5% n/a (RNA) 

• ssRNA 

• Extremely stable structure 

• Retain infectivity at room temp. for ~50 

years 

• Naked RNA is highly unstable like others.

Detailed worked by using 

• X-ray defraction gave details of arrangement of 

protein subunits and RNA in rod. 

• The particles comprises ~2130 subunits that are 

closely packed in a helical array. 

• The pitch of helix is 2.3 (fig.) and the RNA chain is 

compactly coiled in a helix following that of the 

protein subunits 

• There are 49 nt. & 161/3 protein subunits per turn 

• The PO4 of the RNA are at about 4nm from the rod 

axis. 

• The helix of TMV is right handed (Finch, 1972)

TMV architecture 

• Negatively stained particles revealed that : 

• One end of the rod can be seen as concave 

• The other end is convex 

• 3’end of the RNA is at the convex end & 5’ at 

concave end (Wilson wt al. 1976; Butler et al., 

1977) 

• A central canal with a radius of ~2nm becomes 

filled with stain in –vely stained preparations 

• Short Rods: of variable length &

SYMPTOMS OF TMV

Rod shaped particles 

Helix (rod) 

e.g., TMV 

TMV rod is 18 nanometers 

(nm) X 300 nm

PARTICLE STRUCTURE 

TMV rod is 18 nanometers 

(nm) X 300 nm 

• Tobacco mosaic virus is typical, well-studied example 

• Each particle contains only a single molecule of RNA (6395 nt) 

and 2130 copies of the coat protein subunit (158 aa; 17.3 kDa) 

• 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

Tobacco mosaic virus

Properties of coat proteins 

• CP consists of 158 amino acid with a mol. Wt of 

~17-18 KDa. 

• Fibre defraction have determined the structure 

to 2.0oA resolution (Namba et al., 1989) 

• The protein has high proportion of secondary 

structures with 50%of the residues form four a- 

helices and 10% of residues in B-turns. 

• The four closely parallel and antiparallel a- 

helices (residues 20-32, 38-48, 74-88 & 114- 

134) make up the core of the subunits. 

• And the distal end of the four helices are 

connected transversely by a narrow and twisted 

strip of b-sheet.


• The central part of the subunit distal to the b- 

sheet is a cluster aromatic residues (Phe12, 

Trp17, Phe62, Tyr70, Tyr139, Phe144) 

forming a hydrophobic patch. 

• The N- & C- termini of the protein are to the 

outside of the particle 

• The polypeptide chain is in a flexible or 

disordered state below a radius in t particle of 

about 4nm so that no structure is revealed in 

this region.


• One of the reassembly product of TMV 

protein subunit is a double disk containing two 

rings of 17 protein subunits and in this region 

the details of the inter subunit contacts can be 

determined (by X-ray crystallography) (Klug et 

al.; Bloomer et al., 1978). 

• The subunits of the upper ring in the disk are 

flat and in the lower ring are tilted down ward 

toward the centre of the disk with three regions 

of contact between the subunits.

Plant viruses are 

diverse, but not as 

diverse as animal 

viruses – probably 

because of size 

constraints imposed by 

requirement to move 

cell-to-cell through 

plasmodesmata of host 

plants

Viral Morphological Groups 

• Cubic (icosahedral) 

• Helical 

Horne, R. W. & Wildy, P. 

(1961). Symmetry in virus 

architecture. Virology 15, 

348–373

Icosahedral arrangement is typical 

in virus structure 

• An icosahedron has 20 

triangular (equilateral) faces 

(facets), 12 vertices, and a 

5:3:2 axes of rotational 

symmetry

Isometric viruses 

Icosahedron 

(sphere) e.g., BMV

Tobacco necrosis virus, 26 nm in diameter

BROME MOSAIC VIRUS 

• Type member of the 

Bromovirus genus, family 

Bromoviridae 

• Virions are nonenveloped 

icosohedrals (T=3), 26 nm in 

diameter, contain 22% nucleic 

acid and 78% protein 

RNA1 RNA2 RNA3 

RNA4 

• BMV genome is composed 

of three positive sense RNAs 

separately encapsidated 

RNA1 (3.2 kb), RNA2 (2.9 

kb), RNA3 (2.1 kb), RNA4 

(0.9 kb)

Francki, Milne & Hatta. 1985 Atlas of Plant Viruses, vol. I. 

Three-dimensional image of Turnip yellow mosaic virus (TYMV) 

reconstructed from EM

Tobacco mosaic virus 

• First virus crystallized (1946 Stanley was 

awarded the Nobel prize) 

• First demonstration of infectious RNA 

(1950s) 

• First virus to be shown to consist of RNA 

and protein 

• First virus characterized by X-ray 

crystallography to show a helical structure 

• First virus genome to be completely 

sequenced

Tobacco mosaic virus (TMV), 300 nm 

Potato virus Y (PVY), 740 nm

Cocoa swollen shoot virus, 

Badnavirus 

Maize streak virus, 

Geminiviridae

Lect. 6 composition & Architecture of plant viruses

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