Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
16  structures 278  species 2  interactions 310  sequences 9  architectures

Family: ESCRT-II (PF05871)

Summary: ESCRT-II complex subunit

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 "VPS25". More...

VPS25 Edit Wikipedia article

Vacuolar protein sorting 25 homolog (S. cerevisiae)

Rendering based on PDB 2ZME.
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols VPS25; DERP9; EAP20; FAP20
External IDs OMIM610907 MGI106354 HomoloGene6303 GeneCards: VPS25 Gene
RNA expression pattern
PBB GE VPS25 gnf1h00737 at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 84313 28084
Ensembl ENSG00000131475 ENSMUSG00000078656
UniProt Q9BRG1 Q9CQ80
RefSeq (mRNA) NM_032353 NM_026776
RefSeq (protein) NP_115729 NP_081052
Location (UCSC) Chr 17:
40.93 – 40.93 Mb
Chr 11:
101.25 – 101.26 Mb
PubMed search [1] [2]
ESCRT-II complex subunit
PDB 1xb4 EBI.jpg
crystal structure of subunit vps25 of the endosomal trafficking complex escrt-ii
Identifiers
Symbol ESCRT-II
Pfam PF05871
InterPro IPR008570

Vacuolar protein-sorting-associated protein 25 is a protein that in humans is encoded by the VPS25 gene.[1][2]

It is a component of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs).[3] ESCRT-II recruits the transport machinery for protein sorting at MVB.[4] In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo.[5]

ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps36.[6]


References[edit]

  1. ^ Yorikawa C, Shibata H, Waguri S, Hatta K, Horii M, Katoh K, Kobayashi T, Uchiyama Y, Maki M (Mar 2005). "Human CHMP6, a myristoylated ESCRT-III protein, interacts directly with an ESCRT-II component EAP20 and regulates endosomal cargo sorting". Biochem J 387 (Pt 1): 17–26. doi:10.1042/BJ20041227. PMC 1134928. PMID 15511219. 
  2. ^ "Entrez Gene: VPS25 vacuolar protein sorting 25 homolog (S. cerevisiae)". 
  3. ^ Gill DJ, Teo H, Sun J, Perisic O, Veprintsev DB, Emr SD, Williams RL (January 2007). "Structural insight into the ESCRT-I/-II link and its role in MVB trafficking". EMBO J. 26 (2): 600–12. doi:10.1038/sj.emboj.7601501. PMC 1783442. PMID 17215868. 
  4. ^ Teo H, Perisic O, Gonzalez B, Williams RL (October 2004). "ESCRT-II, an endosome-associated complex required for protein sorting: crystal structure and interactions with ESCRT-III and membranes". Dev. Cell 7 (4): 559–69. doi:10.1016/j.devcel.2004.09.003. PMID 15469844. 
  5. ^ Babst M, Katzmann DJ, Snyder WB, Wendland B, Emr SD (August 2002). "Endosome-associated complex, ESCRT-II, recruits transport machinery for protein sorting at the multivesicular body". Dev. Cell 3 (2): 283–9. doi:10.1016/S1534-5807(02)00219-8. PMID 12194858. 
  6. ^ Wernimont AK, Weissenhorn W (December 2004). "Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II". BMC Struct. Biol. 4 (1): 10. doi:10.1186/1472-6807-4-10. PMC 539351. PMID 15579210. 

Further reading[edit]


This article incorporates text from the public domain Pfam and InterPro IPR008570

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

ESCRT-II complex subunit Provide feedback

This family of conserved eukaryotic proteins are subunits of the endosome associated complex ESCRT-II which recruits transport machinery for protein sorting at the multivesicular body (MVB) [1]. This protein complex transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo [1].

Literature references

  1. Babst M, Katzmann DJ, Snyder WB, Wendland B, Emr SD; , Dev Cell 2002;3:283-289.: Endosome-associated complex, ESCRT-II, recruits transport machinery for protein sorting at the multivesicular body. PUBMED:12194858 EPMC:12194858

  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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008570

This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) [PUBMED:17215868]. ESCRT-II recruits the transport machinery for protein sorting at MVB [PUBMED:15469844]. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo [PUBMED:12194858].

ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [PUBMED:15579210].

Domain organisation

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

Loading domain graphics...

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(25)
Full
(310)
Representative proteomes NCBI
(304)
Meta
(1)
RP15
(77)
RP35
(121)
RP55
(179)
RP75
(218)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(25)
Full
(310)
Representative proteomes NCBI
(304)
Meta
(1)
RP15
(77)
RP35
(121)
RP55
(179)
RP75
(218)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(25)
Full
(310)
Representative proteomes NCBI
(304)
Meta
(1)
RP15
(77)
RP35
(121)
RP55
(179)
RP75
(218)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_9765 (release 8.0)
Previous IDs: DUF852;
Type: Family
Author: Moxon SJ, Wood V, Mistry J
Number in seed: 25
Number in full: 310
Average length of the domain: 140.00 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 58.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 22.6 22.4
Noise cut-off 18.5 18.0
Model length: 139
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 2 interactions for this family. More...

ESCRT-II EAP30

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 ESCRT-II domain has been found. There are 16 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.

Loading structure mapping...