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11  structures 2  species 0  interactions 2  sequences 1  architecture

Family: Vpu (PF00558)

Summary: Vpu protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Vpu". More...

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Vpu protein Provide feedback

The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4.

Literature references

  1. Kobinger GP, Mouland AJ, Lalonde JP, Forget J, Cohen EA; , Gene Ther 1997;4:868-874.: Enhancement of retroviral production from packaging cell lines expressing the human immunodeficiency type 1 VPU gene. PUBMED:9338017 EPMC:9338017

  2. Bour S, Schubert U, Strebel K; , J Virol 1995;69:1510-1520.: The human immunodeficiency virus type 1 Vpu protein specifically binds to the cytoplasmic domain of CD4: implications for the mechanism of degradation. PUBMED:7853484 EPMC:7853484

  3. Willbold D, Hoffmann S, Rosch P; , Eur J Biochem 1997;245:581-588.: Secondary structure and tertiary fold of the human immunodeficiency virus protein U (Vpu) cytoplasmic domain in solution. PUBMED:9182993 EPMC:9182993


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008187

The human immunodeficiency virus type 1 Vpu transmembrane protein is required for the induction of degradation human CD4 receptor degradation in the endoplasmic reticulum, and for the enhancement of virus particle release from the plasma membrane of infected cells. The cytoplasmic domain of Vpu directly interacts with the CD4 receptor, targeting it for proteasome degradation [PUBMED:7853484]. 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 [PUBMED:9182993]. The transmembrane domain of Vpu, found towards the N terminus, forms a cation-selective ion channel and is responsible for the enhancement of virus particle release [PUBMED:14529626].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(16)
Full
(2)
Representative proteomes UniProt
(10449)
NCBI
(9286)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(5)
RP75
(6)
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HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(16)
Full
(2)
Representative proteomes UniProt
(10449)
NCBI
(9286)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(5)
RP75
(6)
Alignment:
Format:
Order:
Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(16)
Full
(2)
Representative proteomes UniProt
(10449)
NCBI
(9286)
Meta
(0)
RP15
(4)
RP35
(4)
RP55
(5)
RP75
(6)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Swiss-Prot
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 16
Number in full: 2
Average length of the domain: 79.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 69.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.1 24.4
Noise cut-off 23.9 23.8
Model length: 81
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Vpu domain has been found. There are 11 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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