Virus proteins folds

Despite their extraordinary iversity in sequence, viral genome encode for a limited number of folds. The most prevalent are used for replication or capsid formation.

Viral hallmark proteins (VHP) is a small set of viral protein folds that are widely distributed among viruses and play key roles in replication and capsid formation.

Virus particle

Capsids are protein shells that protect viral genomes. There are about 20 unrelated varieties of these proteins. Most of these folds have evolved independently several times from ancestral proteins of cellular organisms .

Icosahedral capsid

HK97 fold T=1, T=3, T=4
Jelly-roll family
- Single-jelly roll, horizontal T=1, T=3,T=7, T=28
- Single-jelly roll, vertical T=13
- Double-jelly roll, Horizontal/vertical T=13
- Double-jelly roll, vertical T=21->T=277
Duplorna-fold family T=2
Chymotrypsin fold T=4 (Alphavirus)
beta sheet Lenar fold
Retro-CA fold
alpha helical, HBV fold

Helical capsid

SIRV2-like folding
Inovirus-like, plectro-like, Spira-like
TMV-like, Clostero-like, Tymovirales
Poty-like, Amalga-like, Polymyco-like
Baculo-like
Rhabdo-, Pneumo-, Paramyxo-,Borna-, Filo-, Aspi-,Flu-, Hanta-, Bunya-, Phenui-,Arena-, Nairo-

Matrix

ALpha-helix membrane binding
- Retro-Matrix
- Arena-matrix
- Flavi capsid fold
Beta-sheet membrane binding
- Mononegavirus matrix

Fusion

Type I
TypeII
TypeIII

Viral enzymes

Viruses encode only a small set of enzymes and rely heavily on the host cell for most essential biochemical reactions. The viral enzymes that do exist are typically those required for genome replication, as well as proteases involved in processing and maturing viral proteins.

Polymerase

RNA-dependent RNA polymerase (RdRp)
Reverse Transcribing polymerase (RTase)
Protein-primed DNA polymerase

Helicase

Superfamily 3 helicase

Rep

Rolling-circle replication endonuclease

Packaging

genome packaging ATPase-nuclease (large terminase subunit)
portal protein

protease

Chymotrypsin
Papain