Summary: Coatomer (COPI) alpha subunit C-terminus

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COPI Edit Wikipedia article

COPI C-terminal domain

Identifiers

Symbol

COPI_C

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

COPI is a protein complex^[1] that coats vesicles transporting proteins from the cis end of the Golgi complex back to the rough endoplasmic reticulum (ER), where they were originally synthesized and between golgi compartments. This type of transport is termed as retrograde transport, in contrast to the anterograde transport associated with the COPII protein. The name "COPI" refers to the specific coat protein complex that initiates the budding process on the cis-Golgi membrane. The coat consists of large protein subcomplexes that are made of seven different protein subunits.

[edit] Coat proteins

Coat protein, or COPI, is an ADP ribosylation factor (ARF)-dependent adaptor protein involved in membrane traffic.^[2] COPI was first identified in retrograde traffic from the cis-Golgi to the rough endoplasmic reticulum (ER)^[3]^[4] and is the most extensively studied of ARF-dependent adaptors. COPI consists of seven subunits which compose the heptameric protein complex.

The primary function of adaptors is the selection of cargo proteins for their incorporation into nascent carriers. In the case of the adaptor COPI, cargo containing the sorting motif KKXX interact with COPI to form carriers which are transported from the cis-Golgi to the rough ER.^[5]^[6]^[7]^[8] Current views suggest that ARFs are also involved in the selection of cargo for incorporation into carriers.

[edit] Budding process

ADP ribosylation factor (ARF) is a GTPase involved in membrane traffic. There are 30 mammalian ARFs, and 29 in humans due to the loss of ARF2. ARF is post-translationally modified at the N-terminus by the addition of the fatty acid myristate.

ARF cycles between GTP and GDP-bound conformations. In the GTP-bound form, ARF conformation changes such that the myristate and hydrophobic N-terminal become more exposed and associate with the membrane. The interconversion between GTP and GDP bound states is mediated by ARF guanine nucleotide exchange factors (GEFs) and ARF GTPase activating proteins (GAPs). At the membrane, ARF-GTP is hydrolyzed to ARF-GDP by ARF GAPs. Once in the GDP-bound conformation, ARF converts to a less hydrophobic conformation and dissociates from the membrane. Soluble ARF-GDP is converted back to ARF-GTP by GEFs.

1. Luminal proteins: Proteins found in the lumen of the Golgi complex that need to be transported to the lumen of the ER contain the signal peptide KDEL. This sequence is recognized by a membrane-bound KDEL receptor. In yeast, this is Erd2p and in mammals it is KDELR. This receptor then binds to an ARF-GEF, a class of guanine nucleotide exchange factors. This protein in turn binds to the ARF. This interaction causes ARF to exchange its bound GDP for GTP. Once this exchange is made ARF binds to the cytosolic side of the cis-Golgi membrane.

2. Membrane proteins: Transmembrane proteins which reside in the ER contain sorting signals in their cytosolic tails which direct the protein to exit the Golgi and return to the ER. These sorting signals, or motifs, typically contain the amino acid sequence KKXX, which interact with COPI. The order in which adaptor proteins associate with cargo, or adaptor proteins associate with ARFs is unclear, however, in order to form a mature transport carrier coat protein, adaptor, cargo, and ARF must all associate.

Membrane deformation and carrier budding occurs following the collection of interactions described above. The carrier then buds off of the donor membrane, in the case of COPI this membrane is the cis-Golgi, and the carrier moves to the ER where it fuses with the acceptor membrane and its content is expelled.

[edit] References

^ Coat Protein Complex I at the US National Library of Medicine Medical Subject Headings (MeSH)
^ Serafini T, Orci L, Amherdt M, Brunner M, Kahn RA, Rothman JE (1991). "ADP-ribosylation factor is a subunit of the coat of Golgi-derived COP-coated vesicles: a novel role for a GTP-binding protein.". Cell 67 (2): 239–53. doi:10.1016/0092-8674(91)90176-Y. PMID 1680566.
^ Schekman R., Orci L. (1996). "Coat proteins and vesicle budding". Science 271 (5255): 1526–1533. doi:10.1126/science.271.5255.1526. PMID 8599108.
^ Cosson P, Letourneur F (1997). "Coatomer (COPI)-coated vesicles: role in intracellular transport and protein sorting.". Curr Opin Cell Biol 9 (4): 484–7. doi:10.1016/S0955-0674(97)80023-3. PMID 9261053.
^ Letourneur F, Gaynor EC, Hennecke S, Démollière C, Duden R, Emr SD et al. (1994). "Coatomer is essential for retrieval of dilysine-tagged proteins to the endoplasmic reticulum.". Cell 79 (7): 1199–207. doi:10.1016/0092-8674(94)90011-6. PMID 8001155.
^ Sohn K, Orci L, Ravazzola M, Amherdt M, Bremser M, Lottspeich F et al. (1996). "A major transmembrane protein of Golgi-derived COPI-coated vesicles involved in coatomer binding". J Cell Biol 135 (5): 1239–48. doi:10.1083/jcb.135.5.1239. PMC 2121093. PMID 8947548. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2121093/.
^ Sönnichsen B, Watson R, Clausen H, Misteli T, Warren G (1996). "Sorting by COP I-coated vesicles under interphase and mitotic conditions". J Cell Biol 134 (6): 1411–25. doi:10.1083/jcb.134.6.1411. PMC 2120996. PMID 8830771. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2120996/.
^ Orci L, Stamnes M, Ravazzola M, Amherdt M, Perrelet A, Söllner TH et al. (1997). "Bidirectional transport by distinct populations of COPI-coated vesicles". Cell 90 (2): 335–49. doi:10.1016/S0092-8674(00)80341-4. PMID 9244307.

[edit] See also

COPII vesicles
Clathrin vesicles
Glyceraldehyde 3-phosphate dehydrogenase#ER_to_Golgi_transport

Membrane protein: vesicular transport proteins (TC 1F)

Synaptic vesicle

SNARE

Q-SNARE	SNAP25 · SNAP29 Syntaxin (STX1A, STX1B, STX2, STX3, STX4, STX5, STX6, STX7, STX8, STX10, STX11, STX12, STX16, STX17, STX18, STX19) Munc-18: STXBP1 · STXBP2 · STXBP3 · STXBP4 · STXBP5 · STXBP6

R-SNARE	Synaptobrevin/VAMP: VAMP1 · VAMP2 · VAMP3

Synaptotagmin

SYT1 · SYT2 · SYT3 · SYT4 · SYT5 · SYT6 · SYT7 · SYT8 · SYT9 · SYT10 · SYT11 · SYT12 · SYT13 · SYT14 · SYT15 · SYT16 · SYT17

Other

Synaptophysin · Synapsin

Small GTPase: RAB3A

COPI

Coatomer (COPA, COPB1, COPB2, COPE, COPG, COPG2, COPZ1, COPZ2)

Archain

Small GTPase: ARF

COPII

Vesicle formation: SEC23A

Small GTPase: SAR1A

RME/Clathrin

CLTA · CLTB · CLTC

Caveolae

Caveolin (CAV1 · CAV2 · CAV3)

Other/ungrouped

Vesicle formation	Adaptor protein complex 1: AP1AR · AP1B1 · AP1G1 · AP1G2 · AP1M1 · AP1M2 · AP1S1 · AP1S2 · AP1S3 Adaptor protein complex 2: AP2A1 · AP2A2 · AP2B1 · AP2M1 · AP2S1 Adaptor protein complex 3: AP3B1 · AP3B2 · AP3D1 · AP3M1 · AP3M2 · AP3S1 · AP3S2 Adaptor protein complex 4: AP4B1 · AP4E1 · AP4M1 · AP4S1 LMAN1 LYST BLOC-1: DTNBP1 · BLOC153 BLOC-2: HPS3 · HPS5 · HPS6 BLOC-3: HPS1 · HPS4 Coats: Retromer · TIP47

Small GTPase	Dynamin (DNM1, DNM2, DNM3)

Other	EHD protein family: EHD1 · EHD2 · EHD3 · EHD4 Sorting nexins vacuolar protein sorting: VPS13B · VPS33B SYNRG

see also vesicular transport protein disorders
B memb: cead, trns (1A, 1C, 1F, 2A, 3A1, 3A2-3, 3D), othr

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Coatomer (COPI) alpha subunit C-terminus Provide feedback

This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport [1]. Note that many family members also contain the PF04053 domain.

Literature references

Cosson P, Letourneur F; , Curr Opin Cell Biol 1997;9:484-487.: Coatomer (COPI)-coated vesicles: role in intracellular transport and protein sorting. PUBMED:9261053 EPMC:9261053

External database links

PANDIT:	PF06957
Pseudofam:	PF06957
SYSTERS:	COPI_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR010714

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 terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [PUBMED:12893528, PUBMED:9261053]. This domain is found along with the INTERPRO domain.

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.

Cellular component	COPI vesicle coat (GO:0030126)
Molecular function	protein binding (GO:0005515)
Molecular function	structural molecule activity (GO:0005198)
Biological process	intracellular protein transport (GO:0006886)
Biological process	vesicle-mediated transport (GO:0016192)

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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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 (5)	Full (402)	Representative proteomes				NCBI (405)	Meta (8)
	Seed (5)	Full (402)	RP15 (98)	RP35 (152)	RP55 (226)	RP75 (268)	NCBI (405)	Meta (8)
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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, not generated, — not available.

Format an alignment

	Seed (5)	Full (402)	Representative proteomes				NCBI (405)	Meta (8)
	Seed (5)	Full (402)	RP15 (98)	RP35 (152)	RP55 (226)	RP75 (268)	NCBI (405)	Meta (8)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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 (5)	Full (402)	Representative proteomes				NCBI (405)	Meta (8)
	Seed (5)	Full (402)	RP15 (98)	RP35 (152)	RP55 (226)	RP75 (268)	NCBI (405)	Meta (8)
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.

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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.

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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_20121 (release 10.0)

Previous IDs:

none

Type:

Family

Author:

Vella Briffa B

Number in seed:

5

Number in full:

402

Average length of the domain:

362.60 aa

Average identity of full alignment:

35 %

Average coverage of the sequence by the domain:

33.49 %

HMM information

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	19.7	19.7
Trusted cut-off	21.3	20.6
Noise cut-off	19.5	19.1

Model length:

422

Family (HMM) version:

6

Download:

download the raw HMM for this family

Species distribution

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family
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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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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 COPI_C domain has been found. There are 10 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: COPI_C (PF06957)

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