Summary: nodavirus capsid protein
nodavirus capsid protein Provide feedback
The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish.
Nishizawa T, Mori K, Furuhashi M, Nakai T, Furusawa I, Muroga K; , J Gen Virol. 1995;76:1563-1569.: Comparison of the coat protein genes of five fish nodaviruses, the causative agents of viral nervous necrosis in marine fish. PUBMED:9049363 EPMC:9049363
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024292
The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish [PUBMED:9049363].
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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 18 members: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
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_805 (release 23.0)|
|Author:||Mistry J, Coggill P|
|Number in seed:||1|
|Number in full:||510|
|Average length of the domain:||198.40 aa|
|Average identity of full alignment:||76 %|
|Average coverage of the sequence by the domain:||98.69 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|Download:||download the raw HMM for this family|
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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 Capsid-VNN domain has been found. There are 6 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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