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A virus capsid protein alpha-helical domain superfamily
SCOP classification
Superfamily statistics
Functional annotation
| 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
InterPro annotation
| Cross references | IPR008935 SSF48345 Protein matches |
| Abstract | 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 [ 11285214]. 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 [11285213]. |
InterPro database
PDBeMotif information about ligands, sequence and structure motifs
PDBeMotif resource
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) ]
Internal database links
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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.
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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.
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Browse and view proteins in genomes which have
different domain combinations including a A virus capsid protein alpha-helical domain domain.
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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.
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Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
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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.
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Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · UniProtKB KeyWords (KW) · Internal database links ]
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