SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

Home > SCOP hierarchy > Retrovirus capsid protein, N-terminal core domain superfamily

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 term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	0	Least Informative	Direct
Enzyme Commission (EC)	Nucleotidyltransferases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on ester bonds	0	Least Informative	Direct
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	0	Moderately Informative	Direct
Enzyme Commission (EC)	DNA-directed DNA polymerase	0	Moderately Informative	Direct
Enzyme Commission (EC)	Retroviral ribonuclease H	0	Informative	Direct
Enzyme Commission (EC)	Aspartic endopeptidases	0	Informative	Direct
Enzyme Commission (EC)	Exoribonuclease H	0	Informative	Direct
Enzyme Commission (EC)	RNA-directed DNA polymerase	0	Informative	Direct

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferring phosphorus-containing groups	0	Least Informative	Direct
Enzyme Commission (EC)	Hydrolases	0	Least Informative	Direct
Enzyme Commission (EC)	Acting on peptide bonds (peptidases)	0	Moderately Informative	Direct
Enzyme Commission (EC)	Nucleotidyltransferases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Acting on acid anhydrides	0.9467	Moderately Informative	Inherited
Enzyme Commission (EC)	DNA-directed DNA polymerase	0	Informative	Direct
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	0	Informative	Direct
Enzyme Commission (EC)	Exoribonucleases producing 5'-phosphomonoesters	0	Informative	Direct
Enzyme Commission (EC)	In phosphorus-containing anhydrides	0.0000000000000373	Informative	Direct
Enzyme Commission (EC)	dUTP diphosphatase	0	Highly Informative	Direct
Enzyme Commission (EC)	Retroviral ribonuclease H	0	Highly Informative	Direct
Enzyme Commission (EC)	HIV-1 retropepsin	0	Highly Informative	Direct
Enzyme Commission (EC)	RNA-directed DNA polymerase	0	Highly Informative	Direct
Enzyme Commission (EC)	Exoribonuclease H	0	Highly Informative	Direct
Enzyme Commission (EC)	HIV-2 retropepsin	0.00003451	Highly Informative	Direct

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 [ PubMed 9931251, PubMed 10669613].

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 · Enzyme Commission (EC) · Enzyme Commission (EC) ]

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 11 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 11 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 ]