20. Structure of Viruses

virus particle

a complete physical entity that occurs extracellularly and can infect new host cells

• can be referred to as a virion

• this is the thing that would escape when you sneeze/cough etc

what is a virion composed of

• virus genome = nucleic acid

• protein capsid (coat)

• may possess an envelope

• may include replicative enzymes

is the virus genome composed of RNA or DNA

can be either DNA or RNA,

which can either be double stranded or single stranded

what shapes can the protein capsid be

helical, icosahedral, or complex

metastable structures

stable under normal conditions but capable of undergoing a rapid structural change when triggered

• it has to assemble correctly inside the infected cell, then when released into the environment, it has to stay stable

• then when attached/associated with the correct cell in the future, it has to disassemble

why must virions be stable

Outside a host cell, a virus particle must:

• Protect its genome from physical damage

• Survive environmental conditions

• Persist long enough to infect a new host cell

• Remain intact during transmission

If the virion were too fragile, it would fall apart before reaching a new host

why must virions be unstable

Once inside a host cell, the virus must:

• Uncoat (disassemble)

• Release its genome

• Begin replication

If the virion were too stable, the genome would remain trapped inside the capsid and infection could not proceed

what triggers uncoating

Different viruses use different triggers, including:

• Binding to a host-cell receptor

• Low pH in endosomes

• Intracellular enzymes

• Changes in ionic conditions

These cues cause conformational changes in viral proteins that lead to capsid disassembly and genome release.

capsid functions

• protection of nucleic acid: extracellularly or intracellularly

• transport nucleic acid from cell to cell

• provides specificity for attachment (non-enveloped viruses)

• transport nucleic acid to the site of replication

  • packaging

what is extracellular protection

protect the viral genome while the virus is outside the host cell (extracellularly).

why is protection needed extracellularly

Viral nucleic acids (DNA or RNA) are fragile and can be damaged by:

• Nucleases in the environment that degrade nucleic acids

• UV radiation

• Heat

• Chemical damage

• Mechanical stress during transmission between hosts

Without protection, the viral genome would be destroyed before it could infect another cell.

how does the capsid protect the genome extracellularly

The capsid forms a stable protein shell around the genome that:

• Physically shields DNA or RNA from nucleases

• Prevents breakage of the genome

• Protects against environmental stresses

• Maintains genome integrity during transmission

the capsid keeps the genome intact until a suitable host cell is encountered

why is intracellular protection of nucleic acid needed

Once a virus enters a host cell, the genome is still vulnerable to:

• Cellular nucleases that degrade DNA or RNA

• Innate immune sensors that detect foreign nucleic acids

• Mechanical damage during transport through the cytoplasm

• Premature release of the genome before it reaches the correct replication site

how does the capsid provide intracellular protection

1. Protects the genome during transport

• After entry, many viruses do not uncoat immediately, only once they reach the location

2. Prevents genome degradation

   Host cells contain enzymes that destroy free nucleic acids.

3. Prevents premature genome release

   If the genome were released too early:

   • Replication could fail

   • The genome might be degraded

   • The immune system could detect it

   Therefore the capsid maintains the genome in a protected state until specific uncoating signals are received.

4. Helps evade immune detection

   Host cells possess receptors that recognise foreign nucleic acids.

   A capsid can partially shield the genome from these detection systems until uncoating occurs at the appropriate stage of infection. [FMM Struct...26-27.pptx | PowerPoint]

difference between extracellular and intracellular protection

Extracellular	Intracellular
Protects genome during transmission between hosts	Protects genome after cell entry
Prevents environmental damage	Prevents degradation by cellular nucleases
Preserves infectivity	Ensures delivery to replication site
Allows survival outside cells	Prevents premature uncoating

importance of providing specificity for attachment

For a virus to infect a cell, it must first attach to specific receptor molecules on the host cell surface. This specificity is usually provided by capsid proteins (non-enveloped viruses) or viral glycoproteins (enveloped viruses).

how does attachment specificity determine which cells can be infected (tropism)

Viruses can only infect cells that express the correct receptor.

Example:

• HIV binds CD4 and co-receptors such as CCR5/CXCR4.

Therefore, receptor recognition determines the virus's host range and tissue tropism.

how does attachment specificity ensure efficient genome delivery

Specific binding brings the virus into close contact with an appropriate host cell and often triggers:

• Endocytosis

• Membrane fusion

• Capsid conformational changes

• Uncoating

This allows the viral genome to enter the cell successfully

how does attachment specificity avoid wasting viral particles

A virus has limited numbers of particles.

Specific attachment ensures virions bind to cells capable of supporting replication rather than attaching randomly to unsuitable surfaces or cells.

how does attachment specificity influence disease outcome

Changes in attachment proteins can alter:

• Which species a virus infects

• Which tissues are infected

• Disease severity

For example, mutations affecting receptor binding can contribute to viral emergence in new hosts.

importance of transporting nucleic acids to the site of replication

viruses cannot replicate unless their nucleic acid is delivered to the appropriate cellular compartment

Different viruses replicate in different locations:

• Many DNA viruses replicate in the nucleus.

• Most RNA viruses replicate in the cytoplasm.

• Some viruses replicate at specialised viral replication factories.

The viral genome must therefore be transported to the correct site after entry into the cell.

how does the capsid aid in packaging genetic material

nucleic acids are negatively charged, so repels when its folded, so proteins in the capsid neutralise the charge for folding

how are capsids constructed

from sub units:

by repeating many copies of one or a few types of protein subunits that self-assemble into a highly ordered structure

why are capsids made up of sub units instead of one giant protein

viruses have small genomes, so they cannot afford to encode a huge protein large enough to surround the entire genome.

Instead, they encode:

• One capsid protein, or

• A small number of capsid proteins

and then make many copies of those proteins. These copies fit together to form the complete capsid.

in 1956, what did Watson and crick propose about capsid composition

they encode:

• One capsid protein, or

• A small number of capsid proteins

and then make many copies of those proteins. These copies fit together to form the complete capsid

advantages of constructing capsids from sub units

Advantage	Why it helps
Genetic economy	Few genes are needed to build a large structure
Self-assembly	Capsids can form spontaneously from subunits
Structural stability	Symmetrical interactions create a strong shell
Error correction	Damaged subunits can be replaced more easily
Efficient packaging	Large capsids can be built from small proteins

2 dominant, regular structures that most viruses appear as under an electron microscope

• rod like - helical e.g. tobacco mosaic virus

• spherical e.g. polio virushh

how do subunits in helical capsids assemble

In helical viruses:

• Identical protein subunits bind repeatedly along the viral nucleic acid.

• The genome runs through the centre.

• The proteins wind around the genome in a spiral

e.g. tobacco mosaic virus

how do subunits in icosahedral capsids assemble

An icosahedral virus uses many repeated protein subunits arranged with geometric symmetry.

For example, Poliovirus contains:

• 4 different capsid proteins

• 60 copies of each protein

forming a complete icosahedral capsid

how does assembly occur

• Capsid proteins are synthesised by the host cell.

• The proteins form structural subunits.

• Subunits interact through non-covalent forces:

  • Hydrogen bonds

  • Ionic interactions

  • Hydrophobic interactions

• The proteins self-assemble into the final capsid structure.

• The viral genome is packaged during or after assembly.

what are looser helical structures in terms of virion architecture

the protein subunits are arranged in a helix with more space between turns or less tightly packed interactions between neighbouring subunits

• e.g. paramyxovirus

what does the degree of helical packing affect in viruses

1. Flexibility

Looser helices tend to be more flexible.

For example:

• Many animal RNA viruses have flexible helical nucleocapsids.

• This flexibility can help with genome packaging and virus assembly.

2. Genome accommodation

A looser helix can accommodate:

• Larger genomes

• Variations in genome length

This is one reason helical capsids are common among RNA viruses.

3. Envelope association

Many animal helical viruses are also enveloped.

Examples include:

• Influenza virus, Rabies virus, Sendai virus

Their nucleocapsids are often relatively flexible rather than rigid rods.

comparison between structures in tobacco mosaic virus and many animal viruses

TMV has a very tightly packed helical capsid:

• Rigid rod-shaped particle

• Fixed diameter

• Highly ordered structure

By contrast, many animal viruses have:

• More loosely packed helices

• Greater flexibility/flexible nucleocapsid

• Variable particle shapes

nucleocapsid

the viral genome together with its surrounding capsid

what does a nucleocapsid consist of

• viral DNA or RNA

• capsid proteins surrounding the genome

basic viral components for non-enveloped viruses

genome surrounded by capsid (protein coat)

basic viral components for enveloped viruses

genome, capsid, envelope (lipid membrane) with surface proteins embedded

why do many viruses look spherical under the electron microscope

their capsid often has icosahedral symmetry

what does icosahedral symmetry allow the virus to build

build strong capsids from repeated protein subunits

what is icosahedral symmetry

a viral capsid arrangement based on an icosahedron, a structure with 20 triangular faces and 12 vertices. It allows viruses to construct strong, spherical-like capsids from many repeating protein subunits while using minimal genetic information.

icosahedron structure

• 20 triangular faces

• 12 vertices

• 2-fold, 3-fold and 5-fold rotational axes

why do viruses use an icosahedron

Viruses have very small genomes, so they can't encode hundreds of different capsid proteins.

Instead they make:

• One protein (or a few proteins)

• Many identical copies

These proteins self-assemble into an icosahedral shell.

This gives:

✅ Maximum internal volume

✅ High strength

✅ Minimum number of genes needed

✅ Efficient genome packaging

what is 3 fold symmetry

there are 3 different positions you can rotate the shape, and the structure will look the same

why are viral capsids made from repeating subunits

• viral genomes are small and can encode only a limited number of proteins

• these proteins can join together to form a subunit

• many identical subunits then assemble into the capsid

• Repeating subunits provide genetic economy, allow spontaneous self-assembly, generate highly stable symmetrical structures, and efficiently protect the viral genome.

define genome

viral DNA or RNA

capsid

the protein coat around the genomen

nucleocapsid

genome + capsid

envelope

a lipid membrane found around some viruses

• not all viruses have an envelope, but all virions contain a genome

virion

the complete virus particle outside a cell

structure of non-enveloped virus’ and enveloped

methods to study virus structure

• electron microscopy

• cryoelectron microscopy

• cryo electron tomography

• x-ray crystallography

  • difference imaging

how is conventional electron microscopy used to study virus structure

a beam of electrons passes through/around the virus particle, producing an image with much higher resolution than light microscopy,

particles are negatively stained

why do we use electron microscopy and not light

viruses are too small to be seen with a light microscope. Most viruses are between 20–300 nm in diameter, which is below the resolution limit of light microscopy

what can we determine when using conventional EM when studying virus structure

allows researchers to determine:

• Virus size

• Virus shape

• Capsid symmetry

• Presence or absence of an envelope

• Surface structures such as spikes

• capsid architecture

  • helical symmetry (TMV), icosahderal (polio), complex (bacteriophages)

  • important for virus classification and understanding assembly mechanisms

resolution for conventional light microscopy

50-70 A

main features which are identifiable when using EM

morphological units

how is cryo-electron microscopy used to study viral structures

• Virus particles are rapidly frozen.

• Water vitrifies (forms glass-like ice).

• Particles are preserved in a near-native state.

• Thousands of images are collected from different angles.

• Computer software combines them into a 3D reconstruction.

how and why are the virus particles rapidly frozen

Virus particles are suspended in a thin layer of water and rapidly frozen.

This:

• Prevents ice crystal formation

• Preserves the virus in a near-native state

• Avoids structural distortion caused by stains or fixatives

advantages of cryo-EM

• Preserves natural structure

• shows contrast in virus structure itself

• No staining required

• Resolution can reach 2–3 Å

• Can reveal near-atomic details of capsids and glycoproteins

• produces a 3D reconstruction of the virus

how does cryo-EM produce a 3D reconstruction of the virus

by taking thousands to millions of 2D images of virus particles that have been rapidly frozen in vitreous (glass-like) ice,

special software aligns the 2D structures and fit them together

• Computational methods align the resulting 2D projections and combine them to produce a 3D density map

• likely 3D structure

what does EM and Cryo-EM show

• How capsid proteins are arranged

• Number of subunits

• Locations of viral glycoproteins

• Interactions between capsid and genome

This helps explain how viruses assemble, enter cells and uncoat

how is cryo-electron tomography used to study viral structure

1. Rapid freezing

Virus-infected cells or purified virus samples are rapidly frozen so that water forms vitreous ice rather than damaging crystals.

This preserves structures in a near-native state.

2. Collecting a tilt series

Instead of taking a single image, the sample is tilted through a range of angles (for example, from approximately -60° to +60°).

At each angle, a 2D image is recorded, using an electron microscope

3. Computer reconstruction

The images are computationally combined to generate a 3D tomogram (a three-dimensional density map).

• likely 3D structure

like a CT scan, but for frozen cells and viruses

what is cryo-electron tomography useful for

studying viruses inside cells and particles that are not all identical

is the 3D construction completely accurate

it is the most likely structure, so it may not be

when is x-ray crystallography used

to study components of larger viruses

• e.g. adenovirus hexon

what can x-ray crystallography reveal

• Arrangement of capsid proteins

• Structure of viral enzymes

• Structure of viral glycoproteins

• Binding sites for drugs or antibodies

• Atomic interactions between proteins

advantages of x-ray crystallography

Very high resolution (often atomic resolution)

Precise positioning of amino acids

Excellent for studying individual viral proteins

limitations of x-ray crystallography

❌ Requires crystals (which can be difficult to obtain)

❌ Some large or flexible viral structures crystallise poorly

❌ May not perfectly represent the native state in solution

These limitations are one reason cryo-EM has become increasingly important

how can x-ray crystallography and cryo-EM be used together

difference imaging:

combines the x-ray crystal structure of a component of the virus with the cryo-EM images,

this can be used to try and figure out the location of other proteins in the capsid

how was the structure of poliovirus determined

• 1985: x-ray structure was determined

• because it is very small, a crystal structure could be created of the entire virus particle

• 300 A virus particle

• capsid contains 4 proteins (60 copies of each)

structure of poliovirus

• 300 A virus particle

• capsid contains 4 proteins (60 copies of each)

how was the structure of adenovirus determined

its a very complex virus with a lot of proteins inside the capsid and outside, so it was difficult to get an image

• scientists used a mutant virus with a small fibre to solve the crystal structure

what is embedded in the virus membrane

glycoproteins

why do viral enveloped contain a lot of glycoproteins

1. Attachment to host cells

2. Entry into host cells

3. Assembly and budding

4. Determining infectivity

5. Immune interactions

how do glycoproteins embedded in the membrane help with attachment to host cells

Glycoproteins act as receptor-binding proteins.

They recognise and bind specific receptors on the host-cell surface, giving the virus attachment specificity and determining:

• Host range (which species can be infected)

• Tissue tropism (which cell types can be infected)

Without glycoproteins, the virus would be unable to recognise target cells

how do glycoproteins help entry into host cells

Many viral glycoproteins mediate membrane fusion.

After binding a receptor, glycoproteins undergo conformational changes that allow:

• Fusion of the viral envelope with the host membrane

• Release of the nucleocapsid into the cell

For example, influenza haemagglutinin and coronavirus spike proteins are fusion glycoproteins.

how do glycoproteins help assembly and budding

The cytoplasmic domains of glycoproteins interact with viral structural proteins during virus assembly.

This helps:

• Package nucleocapsids

• Promote budding

• Ensure new virions contain the correct envelope proteins

how do glycoproteins embedded determine infectivity

The distribution and number of glycoproteins on the envelope affect:

• How efficiently the virus attaches

• How efficiently fusion occurs

• Overall infectivity

Many enveloped viruses therefore display large numbers of glycoprotein "spikes" on their surface.

how do glycoproteins aid immune interactions

Glycoproteins are exposed on the virion surface and are often the major targets of neutralising antibodies.

Examples:

• Influenza haemagglutinin (HA)

• SARS-CoV-2 spike protein

• HIV gp120

Because antibodies recognise glycoproteins, viruses often evolve changes in these proteins to escape immunity

general structure of the embedded glycoprotein

• on the outside: sugars

• transmembrane region, which spans the lipid bilayer and embeds the protein into the host bilayer

• internal part to associate with other viral proteins to form a capsid

• Ectodomain → outside the virus

• Transmembrane domain → through the membrane

• Cytoplasmic domain → inside the virus

describe the envelope glycoproteins for envelope viruses

• integral membrane proteins

• generally consist of:

  • a large ectodomain

  • a membrane spanning region

  • a small internal cytosolic domain

• generally oligomeric

integral membrane protein?

typically cross the membrane

oligomeric

Made up of a small number of repeating subunits (monomers) that associate together to form a larger structure.

• Monomer = one subunit

• Oligomer = a few subunits joined together

• Polymer = many subunits joined together

oligomeric glycoprotein

means the glycoprotein is not a single protein chain acting alone.

Instead, several copies assemble together.

For example:

• Influenza haemagglutinin (HA) = trimer

• SARS-CoV-2 spike protein = trimer

• Many viral fusion proteins function as oligomers

importance of the oligomeric structure

• Increases stability

• Creates receptor-binding sites

• Allows membrane fusion

• Helps virus assembly

ectodomain

• binds to cell surface receptors

• is recognised by antibodies

  • often the main target of neutralising antibodies

• mediates fusion with cell membranes

its on the outside

cytosolic domain

involved in interactions with the viral core

• Ectodomain → outside the virus

• Transmembrane domain → through the membrane

• Cytoplasmic domain → inside the virus

how are virus assembled

• formation of individual structural units of the protein shell from one or several viral proteins

• assembly of the protein shell by interaction of the structural units

• selective packaging of the nucleic acid genome and other essential virion components

• acquisition of an envelope, if needed

• released from the host cell

• some undergo virion maturation

virion maturation?

• the final stage of virus assembly in which a newly formed virus particle undergoes structural changes to become fully infectious

• A virus particle may be assembled, but it is often not yet capable of infecting another cell. Maturation converts an immature virion into a mature infectious virion

why is maturation necessary

After assembly:

• Capsid proteins may be in a precursor form.

• The genome may not be fully packaged.

• Fusion proteins may not yet be active.

• The particle may be structurally incomplete.

Maturation creates the final architecture needed for infection

what happens during maturation

depending on the virus, maturation can involve:

1. proteolytic cleavage

2. capsid reorganisation

3. activation of fusion proteins

4. genome condensation and packaging changes

proteolytic cleavage?

Viral or host proteases cut precursor proteins into their mature forms.

This can:

• Stabilise the capsid

• Activate viral proteins

• Create infectious particles

caused reorganisation

Capsid proteins may change shape and rearrange into their final structure.

This often increases:

• Stability

• Genome protection

• Infectivity

activation of fusion proteins

For many enveloped viruses, glycoproteins are produced as inactive precursors.

During maturation they are cleaved into active fusion proteins capable of mediating entry into new host cells.

genome condensation and packaging changes

some viruses undergo genome reorganisation that prepares the nucleic acid for infection

example of HIV maturing

• Immature HIV particles bud from the cell.

• Viral protease cleaves Gag and Gag-Pol polyproteins.

• The internal structure rearranges.

• The mature conical capsid forms.

Without maturation:

✅ Particle is produced

❌ Particle is largely non-infectious

what does it mean when we say particles are assembled in a defined process

virus assembly is not random.

The components come together in a specific, ordered sequence that reliably produces a functional virion (there is an organised pathway)

defined process for virus assembly

• Viral proteins are synthesised

• Capsid subunits form

• Capsid assembly occurs

• The genome is packaged

• An envelope is acquired (if the virus is enveloped)

• Maturation occurs

• The virion is released

why does assembly need to be defined

If assembly were random:

• Wrong proteins could be incorporated

• The genome might not be packaged

• Capsids might form incorrectly

• The resulting particles would not be infectious

A defined assembly pathway ensures that virtually every completed particle has:

✅ the correct genome

✅ the correct proteins

✅ the correct structure

✅ the ability to infect another cell

what are structurally complex viruses and an example

• viruses whose architecture cannot be described as simply helical or icosahedral.

• They possess additional structural components or more elaborate organisation than the two major capsid symmetry type