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28  structures 423  species 5  interactions 3508  sequences 60  architectures

Family: Snf7 (PF03357)

Summary: Snf7

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

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This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins [1]. A few archaeal sequences are also present within this family.

Literature references

  1. Babst M, Katzmann DJ, Estepa-Sabal EJ, Meerloo T, Emr SD; , Dev Cell 2002;3:271-282.: Escrt-III: an endosome-associated heterooligomeric protein complex required for mvb sorting. PUBMED:12194857 EPMC:12194857

  2. Teo H, Perisic O, Gonzalez B, Williams RL; , Dev Cell 2004;7:559-569.: ESCRT-II, an endosome-associated complex required for protein sorting: crystal structure and interactions with ESCRT-III and membranes. PUBMED:15469844 EPMC:15469844

  3. Peck JW, Bowden ET, Burbelo PD; , Biochem J 2004;377:693-700.: Structure and function of human Vps20 and Snf7 proteins. PUBMED:14583093 EPMC:14583093


This tab holds annotation information from the InterPro database.

InterPro entry IPR005024

Snf7 family members are small coil-coiled proteins that share protein sequence similarity with budding yeast Snf7, which is part of the ESCRT-III complex that is required for endosome-mediated trafficking via multivesicular body (MVB) formation and sorting [PUBMED:15086794].

Proteins in this entry also includes human CHMPs (charged multivesicular body proteins), budding yeast Did4/Did2 and Arabidopsis vacuolar protein sorting-associated proteins.

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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Pfam Clan

This family is a member of clan PspA (CL0235), which has the following description:

This clan includes PspA like proteins that are transcriptional activators as well as Snf7, a protein involved in cellular trafficking.

The clan contains the following 2 members:

PspA_IM30 Snf7

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
(33)
Full
(3508)
Representative proteomes UniProt
(8139)
NCBI
(8006)
Meta
(47)
RP15
(1047)
RP35
(1950)
RP55
(2848)
RP75
(3462)
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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
(33)
Full
(3508)
Representative proteomes UniProt
(8139)
NCBI
(8006)
Meta
(47)
RP15
(1047)
RP35
(1950)
RP55
(2848)
RP75
(3462)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(33)
Full
(3508)
Representative proteomes UniProt
(8139)
NCBI
(8006)
Meta
(47)
RP15
(1047)
RP35
(1950)
RP55
(2848)
RP75
(3462)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Pfam-B_1641 (release 6.6)
Previous IDs: DUF279; SNF7; ESCRT-III;
Type: Family
Author: Mifsud W, Moxon SJ, Mistry J, Wood V
Number in seed: 33
Number in full: 3508
Average length of the domain: 168.80 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 68.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.8 21.7
Model length: 173
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 5 interactions for this family. More...

ESCRT-II MIT Vta1 Snf7 ESCRT-II

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 Snf7 domain has been found. There are 28 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 seqence.

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