Summary: Calicivirus coat protein C-terminal
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Calicivirus coat protein C-terminal Provide feedback
This is the calicivirus coat protein (PF00915) C-terminal region.
This tab holds annotation information from the InterPro database.
InterPro entry IPR013643
Bovine calicivirus is a positive-stranded ssRNA viruses that cause gastroenteritis [PUBMED:1840711]. The calicivirus genome contains two open reading frames, ORF1 and ORF2 [PUBMED:8892921, PUBMED:8642693]. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity. The regions of the poly-protein in which these activities lie are similar to proteins produced by the picornaviruses [PUBMED:8892921, PUBMED:1551442]. ORF2 encodes a structural protein [PUBMED:8892921]. This signature finds ORF2, the structural coat protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely those classified as small round structured viruses (SRSVs) and those classed as non-SRSVs.
Rabbit hemorrhagic disease virus (RHDV) which causes a highly contagious disease of wild and domestic rabbits belongs to the family Caliciviridae [PUBMED:16733562]. The capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry. It is about 38nm in diameter and consists of 180 capsid proteins. The capsid encapsulates the genomic RNA and VP2 proteins and attaches the virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells. The Shell domain (S domain) contains elements essential for the formation of the icosahedron. The Protruding domain (P domain) is divided into sub-domains P1 and P2. An hypervariable region in P2 is thought to play an important role in receptor binding and immune reactivity.
This is the calicivirus coat protein (INTERPRO) C-terminal region.
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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.
The clan contains the following 26 members: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
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Curation and family details
|Seed source:||Pfam-B_108 (release 18.0)|
|Number in seed:||29|
|Number in full:||1|
|Average length of the domain:||224.00 aa|
|Average identity of full alignment:||100 %|
|Average coverage of the sequence by the domain:||42.26 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Calici_coat_C domain has been found. There are 198 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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