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.

Replication folds

RNA-dependent RNA polymerase (RdRp)
Reverse Transcribing polymerase (RTase)
Protein-primed DNA polymerase
Superfamily 3 helicase
Rolling-circle replication endonuclease

Capsid folds

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

Single-jelly roll, horizontal T=1
BTV-fold T=2
Single/double-jelly roll vertical T=13
HK97 fold T=1, T=3, T=4
beta sheet Lenar fold
Retro-CA fold
Double jelly roll, vertical T=21->T=277
Chy-PRO, toga fold
alpha helical, Flavi fold
alpha helical, HBV fold

helical capsid

Adnaviria (SIRV2-like folding)
Monodnaviria (Inovirus-like, plectro-like, Spira-like)
Kitriniviricota (TMV-like, Clostero-like, Tymovirales)
Pisuviricota (Poty-like, Amalga-like, Polymyco-like)
Baculo-like
Negarnaviricota (Rhabdo-, Pneumo-, Paramyxo-,Borna-, Filo-, Aspi-,Flu-, Hanta-, Bunya-, Phenui-,Arena-, Nairo-)

Fusion protein folds

Type I
TypeII
TypeIII

Virion formation folds

genome packaging ATPase-nuclease (large terminase subunit)
portal protein
capsid maturation protease
Matrix proteins