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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 0 19
Proteins 372 0 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)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00003403Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral release from host cell0Highly InformativeDirect
Biological processEukaryotic host translation shutoff by virus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0.00000000009353Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentViral matrix protein0Highly InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.00000000001195Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.000009578Least InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationMultifunctional enzyme0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation0.00000003918Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW 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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]