Summary: emp24/gp25L/p24 family/GOLD
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emp24/gp25L/p24 family/GOLD Provide feedback
Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in [2]. The GOLD domain is always found combined with lipid- or membrane-association domains [2].
Literature references
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Dominguez M, Dejgaard K, Fullekrug J, Dahan S, Fazel A, Paccaud JP, Thomas DY, Bergeron JJ, Nilsson T; , J Cell Biol 1998;140:751-765.: gp25L/emp24/p24 protein family members of the cis-Golgi network bind both COP I and II coatomer. PUBMED:9472029 EPMC:9472029
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Anantharaman V, Aravind L; , Genome Biol 2002;3:research0023.: The GOLD domain, a novel protein module involved in Golgi function and secretion. PUBMED:12049664 EPMC:12049664
Internal database links
SCOOP: | SdrD_B |
External database links
SCOP: | 1m23 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR009038
The GOLD (for Golgi dynamics) domain is a protein module found in several eukaryotic Golgi and lipid-traffic proteins. It is typically between 90 and 150 amino acids long. Most of the size difference observed in the GOLD-domain superfamily is traceable to a single large low-complexity insert that is seen in some versions of the domain. With the exception of the p24 proteins, which have a simple architecture with the GOLD domain as their only globular domain, all other GOLD-domain proteins contain additional conserved globular domains. In these proteins, the GOLD domain co-occurs with lipid-, sterol- or fatty acid-binding domains such as PH, CRAL-TRIO, FYVE oxysterol binding- and acyl CoA-binding domains, suggesting that these proteins may interact with membranes. The GOLD domain can also be found associated with a RUN domain, which may have a role in the interaction of various proteins with cytoskeletal filaments. The GOLD domain is predicted to mediate diverse protein-protein interactions [PUBMED:12049664]. A secondary structure prediction for the GOLD domain reveals that it is likely to adopt a compact all-beta-fold structure with six to seven strands. Most of the sequence conservation is centred on the hydrophobic cores that support these predicted strands. The predicted secondary-structure elements and the size of the conserved core of the domain suggests that it may form a beta- sandwich fold with the strands arranged in two beta sheets stacked on each other [PUBMED:12049664].
Some proteins known to contain a GOLD domain are listed below:
- Eukaryotic proteins of the p24 family.
- Animal Sec14-like proteins. They are involved in secretion.
- Human Golgi resident protein GCP60. It interacts with the Golgi integral membrane protein Giantin.
- Yeast oxysterol-binding protein homologue 3 (OSH3).
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 GOLD-like (CL0521), which has the following description:
This superfamily is characterised by proteins with a sandwich structure of 8 strands in 2 sheets as a jelly-roll. The structure has similarity to the Nucleoplasmin-like/VP fold. The members are all involved in golgi trafficking.
The clan contains the following 2 members:
EMP24_GP25L GOLD_2Alignments
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...
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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 (215) |
Full (6760) |
Representative proteomes | UniProt (9975) |
NCBI (10945) |
Meta (11) |
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RP15 (1862) |
RP35 (3708) |
RP55 (5354) |
RP75 (6555) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (215) |
Full (6760) |
Representative proteomes | UniProt (9975) |
NCBI (10945) |
Meta (11) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1862) |
RP35 (3708) |
RP55 (5354) |
RP75 (6555) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_803 (release 3.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 215 |
Number in full: | 6760 |
Average length of the domain: | 175.80 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 74.36 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 182 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
EMP24_GP25LStructures
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 EMP24_GP25L domain has been found. There are 15 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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