A virus capsid protein alpha-helical domain superfamily
|General category ||Other|
|Detailed category ||Viral proteins|
Document: Function annotation of SCOP domain superfamilies
UniProtKB KeyWords (KW)(show details)
Highlighted in gray are those with FDR_all>0.001
Document: KW annotation of SCOP domains
|Cross references ||IPR008935 SSF48345 Protein matches|
The capsid of spherical viruses is built from a limited number of proteins and often displays icosahedral symmetry. Rotaviruses have a segmented double-stranded RNA genome enclosed in a complex capsid formed by three concentric protein layers. The proteins forming the capsid are VP2 (internal layer, with triangulation T = 1 and an asymmetric dimer in the icosahedral repeating unit), VP6 (intermediate layer, T = 13 symmetry), VP7 (external layer, T = 13) and VP4, which forms a spike inserted in the outermost two layers. The major capsid protein VP6 self-assembles into spherical or helical particles mainly depending upon pH. VP6 assemblies arise from different pickings of a unique dimer of trimers. The repeating unit of the helix contains a pair of trimers related by a radial dyad . The VP6 trimer is composed of two domains: a head (external) and a base (internal), leaving a central cavity, these are formed by a distal beta-barrel domain and a proximal alpha-helical domain, which interact with the outer and inner layer of the virion, respectively .
PDBeMotif information about ligands, sequence and structure motifs
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Internal database links
Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry
out SCOP domain assignments to all genomes at the superfamily level.
Alignments of sequences to 3 models
in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical
are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.
Browse and view proteins in genomes which have
different domain combinations including a A virus capsid protein alpha-helical domain domain.
Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.
Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
There are 3 hidden Markov models representing the A virus capsid protein alpha-helical domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) · Internal database links ]