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0  structures 301  species 0  interactions 351  sequences 9  architectures

Family: Coatamer_beta_C (PF07718)

Summary: Coatomer beta C-terminal region

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Coatomer beta C-terminal region Provide feedback

This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal PF01602 domain.

Literature references

  1. Hirst J, Bright NA, Rous B, Robinson MS;, Mol Biol Cell. 1999;10:2787-2802.: Characterization of a fourth adaptor-related protein complex. PUBMED:10436028 EPMC:10436028

  2. Takatsu H, Futatsumori M, Yoshino K, Yoshida Y, Shin HW, Nakayama K;, Biochem Biophys Res Commun. 2001;284:1083-1089.: Similar subunit interactions contribute to assembly of clathrin adaptor complexes and COPI complex: analysis using yeast three-hybrid system. PUBMED:11409905 EPMC:11409905


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011710

Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer [PUBMED:15261670]. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins [PUBMED:14690497]. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi [PUBMED:11208122]. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes [PUBMED:17041781]. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits.

This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway [PUBMED:12893528].

More information about these proteins can be found at Protein of the Month: Clathrin [PUBMED:].

Gene Ontology

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

Domain organisation

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Alignments

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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
(25)
Full
(351)
Representative proteomes NCBI
(354)
Meta
(8)
RP15
(90)
RP35
(147)
RP55
(213)
RP75
(255)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(25)
Full
(351)
Representative proteomes NCBI
(354)
Meta
(8)
RP15
(90)
RP35
(147)
RP55
(213)
RP75
(255)
Alignment:
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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
(25)
Full
(351)
Representative proteomes NCBI
(354)
Meta
(8)
RP15
(90)
RP35
(147)
RP55
(213)
RP75
(255)
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: Yeats C
Previous IDs: DUF1606;
Type: Domain
Author: Yeats C
Number in seed: 25
Number in full: 351
Average length of the domain: 138.40 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 15.21 %

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 25.0 25.0
Trusted cut-off 36.2 30.3
Noise cut-off 23.6 22.6
Model length: 141
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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