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Retrovirus capsid protein, N-terminal core domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Retrovirus capsid protein, N-terminal core domain [ 47942]
Superfamily:   Retrovirus capsid protein, N-terminal core domain [ 47943]
Families:   Retrovirus capsid protein, N-terminal core domain [ 47944] (5)


Superfamily statistics
Genomes (21) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 372 71,776 19
Proteins 372 71,770 19


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides0.000000000000003691InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)dUTP diphosphatase0Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00003416Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008919 SSF47943 Protein matches
Abstract

The Gag polyprotein from retroviruses is processed by viral protease to produce the major structural proteins, including the capsid protein. The newly formed capsid protein rearranges to form the capsid core particle that surrounds the viral genome of the mature virus. The capsid is composed of two domains, the N-terminal domain (NTD), which contributes to viral core formation, and the C-terminal domain (CTD), which is required for capsid dimerisation, Gag oligomerization and viral formation. The NTD is composed of a five-helix bundle [PubMed9931251, PubMed10669613].


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

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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 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 Retrovirus capsid protein, N-terminal core 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 6 hidden Markov models representing the Retrovirus capsid protein, N-terminal core 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]