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RNA bacteriophage capsid protein superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   RNA bacteriophage capsid protein [ 55404]
Superfamily:   RNA bacteriophage capsid protein [ 55405]
Families:   RNA bacteriophage capsid protein [ 55406] (5)


Superfamily statistics
Genomes (0) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 0 321 14
Proteins 0 321 13


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR015954 SSF55405 Protein matches
Abstract

This entry represents capsid coat proteins from a variety of RNA bacteriophages, including Bacteriophage MS2, Bacteriophage GA, Bacteriophage fr, Bacteriophage Q-beta and Bacteriophage PP7. These capsid coat proteins share a similar structure, consisting of a 6-stranded beta-sheet followed by two helices. Capsid proteins form the bacteriophage coat that encapsidates the viral RNA. In Bacteriophage MS2, 180 copies of this protein form the virion shell and control two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication [PubMed7523953].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation ]

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 6 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 RNA bacteriophage capsid protein 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 6 hidden Markov models representing the RNA bacteriophage capsid protein 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 · Internal database links ]