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790  structures 9475  species 17  interactions 53300  sequences 144  architectures

Clan: Viral_ssRNA_CP (CL0055)

Summary

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 17 families and the total number of domains in the clan is 53300. The clan was built by RD Finn.

Members

This clan contains the following 17 member families:

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...

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Alignments

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

Pfam family Num. domains Alignment
Rhv (PF00073) 28435 (53.3%) View
Calici_coat (PF00915) 9404 (17.6%) View
TT_ORF1 (PF02956) 3965 (7.4%) View
SP2 (PF03014) 3837 (7.2%) View
Birna_VP2 (PF01766) 2317 (4.3%) View
Circo_capsid (PF02443) 1556 (2.9%) View
Luteo_coat (PF00894) 1368 (2.6%) View
Viral_coat (PF00729) 577 (1.1%) View
Cucumo_coat (PF00760) 531 (1.0%) View
Capsid-VNN (PF11729) 443 (0.8%) View
Nepo_coat (PF03391) 339 (0.6%) View
CRPV_capsid (PF08762) 192 (0.4%) View
Tymo_coat (PF00983) 153 (0.3%) View
Como_LCP (PF02247) 129 (0.2%) View
Peptidase_A21 (PF03566) 29 (0.1%) View
Bromo_coat (PF01318) 16 (0.0%) View
Peptidase_A6 (PF01829) 9 (0.0%) View
Total: 17 Total: 53300 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

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

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Interactions

There are 17 interactions for this clan. More...

Interacting families
A B
Viral_coat Viral_coat
Carmo_coat_C
CRPV_capsid Rhv
Rhv Ldl_recept_a
Rhv
Sushi
Pico_P1A
CRPV_capsid
VP4_2
Nepo_coat Nepo_coat_C
Nepo_coat_N
Peptidase_A21 Peptidase_A21
Calici_coat Calici_coat
Calici_coat_C
Tymo_coat Tymo_coat
Bromo_coat Bromo_coat
Cucumo_coat Cucumo_coat

Structures

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.

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