SUPERFAMILY 1.75 HMM library and genome assignments server


HIV-1 VPU cytoplasmic domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   HIV-1 VPU cytoplasmic domain [ 57646]
Superfamily:   HIV-1 VPU cytoplasmic domain [ 57647]
Families:   HIV-1 VPU cytoplasmic domain [ 57648]


Superfamily statistics
Genomes (0) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 0 19,534 1
Proteins 0 19,534 1


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processApoptosis0Moderately InformativeDirect
Biological processViral immunoevasion5.128e-11InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentHost membrane0InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009032 SSF57647 Protein matches
Abstract

The human immunodeficiency virus type 1 Vpu transmembrane protein acts in the degradation of human CD4 receptor in the endoplasmic reticulum, and in the enhancement of virus particle release from the plasma membrane of infected cells. The cytoplasmic domain of Vpu is responsible for direct interaction with and degradation of the C4 receptor. The cytoplasmic domain encompasses the C-terminal half of the 81-residue protein, and is comprised of a few helical turns without an apparent hydrophobic core [PubMed9182993].


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 · 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 1 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 HIV-1 VPU cytoplasmic 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 1 hidden Markov models representing the HIV-1 VPU cytoplasmic 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 · UniProtKB KeyWords (KW) · Internal database links ]