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Retrovirus capsid dimerization domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Acyl carrier protein-like [ 47335] (3)
Superfamily:   Retrovirus capsid dimerization domain-like [ 47353] (2)
Families:   Retrovirus capsid protein C-terminal domain [ 47354] (4)
  SCAN domain [ 140466] (2)


Superfamily statistics
Genomes (75) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,796 61,706 16
Proteins 2,788 61,684 16


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0.004278 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9787 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.5123 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.3263 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.3423 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4562 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0002202 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.008757 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00151 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.009168 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.06755 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2413 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00354 Moderately Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0002619 Informative Direct
Biological Process (BP) DNA metabolic process 0.0007767 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0009074 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.001858 Informative Inherited
Biological Process (BP) chromosome organization 0.00549 Informative Inherited
Biological Process (BP) anatomical structure homeostasis 0.000001842 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00004499 Highly Informative Direct
Molecular Function (MF) binding 0.00000000001058 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000000001041 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.0306 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.00000000000004736 Informative Direct
Molecular Function (MF) zinc ion binding 0.0005011 Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0001551 Highly Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0.0004457 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.003603 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.3046 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.05978 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000003181 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.001355 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.02275 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.01663 Highly Informative Inherited

Document: GO annotation of SCOP domains

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0.0000000000005497Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.000000000008229Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentChromosome0.01435InformativeInherited
Cellular componentHost endosome0Highly InformativeDirect
Cellular componentTelomere0.0000000004666Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0.00000002064Least InformativeDirect
Post-translational modificationTransferase0.2489Least InformativeInherited
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationRepressor0.000000001394Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationMethylation0.000002473Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008916 SSF47353 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 CTD contains the major homology region (MHR), a stretch of 20 amino acids that is conserved across retroviruses and is essential for viral assembly, maturation and infectivity. The CTD is composed of a bundle of four helices in an up and down arrangement, where helix 3 is shorter than the others [PubMed9346481, 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 · Gene Ontology (high-coverage) · 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 7 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 dimerization domain-like 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 7 hidden Markov models representing the Retrovirus capsid dimerization domain-like 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]