Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
949  structures 14409  species 30  interactions 82242  sequences 160  architectures

Clan: Viral_ssRNA_CP (CL0055)


Positive stranded ssRNA viruses coat protein Add an annotation

The clan contains a set of viral coat protein families and peptidase A6. The only known peptidase activity is an autolytic cleavage releasing a 44-residue C-terminal fragment. The reaction is very slow and only occurs within the assembled virion. There is debate whether this is actually a true peptidase. The virion with these coat or capsid proteins are icosahedral viruses containing sixty triangular coat protein units, each unit consisting of three proteins. The coat protein consists of two subdomains, an eight-stranded beta-barrel on the surface and a three-helix bundle on the inner face.

This clan contains 18 families and the total number of domains in the clan is 82242. The clan was built by RD Finn.


This clan contains the following 18 member families:

Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Capsid-VNN Circo_capsid Como_LCP CRPV_capsid Cucumo_coat Luteo_coat Nepo_coat Peptidase_A21 Peptidase_A6 Rhv SP2 TT_ORF1 Tymo_coat Viral_coat

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...


The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
Rhv (PF00073) 45340 (55.1%) View
Calici_coat (PF00915) 14558 (17.7%) View
SP2 (PF03014) 6582 (8.0%) View
TT_ORF1 (PF02956) 4098 (5.0%) View
Birna_VP2 (PF01766) 2744 (3.3%) View
Circo_capsid (PF02443) 2110 (2.6%) View
Astro_capsid_N (PF03115) 2011 (2.4%) View
Luteo_coat (PF00894) 1688 (2.1%) View
Cucumo_coat (PF00760) 750 (0.9%) View
Viral_coat (PF00729) 672 (0.8%) View
Capsid-VNN (PF11729) 510 (0.6%) View
Nepo_coat (PF03391) 441 (0.5%) View
CRPV_capsid (PF08762) 303 (0.4%) View
Tymo_coat (PF00983) 224 (0.3%) View
Como_LCP (PF02247) 159 (0.2%) View
Peptidase_A21 (PF03566) 27 (0.0%) View
Bromo_coat (PF01318) 16 (0.0%) View
Peptidase_A6 (PF01829) 9 (0.0%) View
Total: 18 Total: 82242 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...