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.
2220  structures 88  species 34  interactions 176  sequences 56  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 26 families and the total number of domains in the clan is 176. The clan was built by RD Finn.


This clan contains the following 26 member families:

Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Calici_coat_C Capsid-VNN Carmo_coat_C Circo_capsid Como_LCP Como_SCP CRPV_capsid Cucumo_coat Dicistro_VP4 Luteo_coat Nepo_coat Nepo_coat_C Nepo_coat_N Peptidase_A21 Peptidase_A6 Pico_P1A Rhv SP2 TT_ORF1 Tymo_coat Viral_coat VP4_2

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) 76 (43.2%) View
TT_ORF1 (PF02956) 15 (8.5%) View
Viral_coat (PF00729) 14 (8.0%) View
Pico_P1A (PF02226) 7 (4.0%) View
Calici_coat (PF00915) 7 (4.0%) View
VP4_2 (PF08935) 6 (3.4%) View
Luteo_coat (PF00894) 6 (3.4%) View
CRPV_capsid (PF08762) 5 (2.8%) View
Dicistro_VP4 (PF11492) 4 (2.3%) View
Como_SCP (PF02248) 4 (2.3%) View
Peptidase_A21 (PF03566) 4 (2.3%) View
Como_LCP (PF02247) 4 (2.3%) View
Birna_VP2 (PF01766) 4 (2.3%) View
Tymo_coat (PF00983) 3 (1.7%) View
Pfam family Num. domains Alignment
Nepo_coat_N (PF03689) 2 (1.1%) View
SP2 (PF03014) 2 (1.1%) View
Cucumo_coat (PF00760) 2 (1.1%) View
Circo_capsid (PF02443) 2 (1.1%) View
Astro_capsid_N (PF03115) 2 (1.1%) View
Nepo_coat_C (PF03688) 1 (0.6%) View
Carmo_coat_C (PF08462) 1 (0.6%) View
Calici_coat_C (PF08435) 1 (0.6%) View
Capsid-VNN (PF11729) 1 (0.6%) View
Peptidase_A6 (PF01829) 1 (0.6%) View
Nepo_coat (PF03391) 1 (0.6%) View
Bromo_coat (PF01318) 1 (0.6%) View
Total: 26 Total: 176 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...