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98  structures 1475  species 0  interactions 15242  sequences 238  architectures

Family: Clat_adaptor_s (PF01217)

Summary: Clathrin adaptor complex small chain

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 "Clathrin adaptor proteins". More...

Clathrin adaptor proteins Edit Wikipedia article

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Clathrin adaptor complex small chain Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022775

Proteins synthesized 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 ].

Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [ PUBMED:17449236 ]. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis [ PUBMED:12858162 ].

While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins [ PUBMED:14690497 ]. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes [ PUBMED:17041781 ]. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits.

This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [ PUBMED:8157009 , PUBMED:8373805 , PUBMED:8157009 , PUBMED:9002613 ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [ PUBMED:8276893 , PUBMED:14729954 ].

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 PF (CL0431), which has the following description:

The families here all show the Profilin-like fold, and represent both the Profilin (actin-binding protein) (55770) and the Roadblock/LC7 domain-type (103196) superfamilies.

The clan contains the following 21 members:

Clat_adaptor_s FNIP_N Fuz_longin_1 Fuz_longin_2 Fuz_longin_3 Intu_longin_1 Intu_longin_2 Intu_longin_3 LAMTOR5 Longin Longin_2 MAPKK1_Int Nyv1_N Profilin Robl_LC7 Sedlin_N SLM4 SRP-alpha_N SRX Sybindin uDENN

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 and the UniProtKB 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
(7)
Full
(15242)
Representative proteomes UniProt
(25878)
RP15
(2630)
RP35
(6518)
RP55
(11969)
RP75
(16158)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(7)
Full
(15242)
Representative proteomes UniProt
(25878)
RP15
(2630)
RP35
(6518)
RP55
(11969)
RP75
(16158)
Alignment:
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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
(7)
Full
(15242)
Representative proteomes UniProt
(25878)
RP15
(2630)
RP35
(6518)
RP55
(11969)
RP75
(16158)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Prosite
Previous IDs: Clathrin_adapt_s;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 7
Number in full: 15242
Average length of the domain: 134.10 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 48.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 142
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Selections

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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 Clat_adaptor_s domain has been found. There are 98 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K302 View 3D Structure Click here
A0A0G2L3C4 View 3D Structure Click here
A0A0P0V2K3 View 3D Structure Click here
A0A0R0E881 View 3D Structure Click here
A0A0R0L8Y1 View 3D Structure Click here
A0A0R4ILF8 View 3D Structure Click here
A0A0R4IRS1 View 3D Structure Click here
A0A0R4J4X2 View 3D Structure Click here
A0A0R4J5K6 View 3D Structure Click here
A0A144A372 View 3D Structure Click here
A0A1D5NSU3 View 3D Structure Click here
A0A1D6EES9 View 3D Structure Click here
A0A1D6FET9 View 3D Structure Click here
A0A1D6FQ28 View 3D Structure Click here
A0A1D6FRR0 View 3D Structure Click here
A0A1D6GG67 View 3D Structure Click here
A0A1D6I669 View 3D Structure Click here
A0A1D6L6Q4 View 3D Structure Click here
A0A1D6L964 View 3D Structure Click here
A0A1D6MW96 View 3D Structure Click here
A0A1D6MY50 View 3D Structure Click here
A0A1D6N513 View 3D Structure Click here
A0A1D6PFK8 View 3D Structure Click here
A0A1D8PND9 View 3D Structure Click here
A0A2R8QEG9 View 3D Structure Click here
A0A2R8RMS1 View 3D Structure Click here
A2CG10 View 3D Structure Click here
A4I4K2 View 3D Structure Click here
A4IA12 View 3D Structure Click here
A4IAR2 View 3D Structure Click here
A9JRS9 View 3D Structure Click here
B0G185 View 3D Structure Click here
B2GV08 View 3D Structure Click here
B4FEL3 View 3D Structure Click here
B4FQ20 View 3D Structure Click here
B4FTQ9 View 3D Structure Click here
B5DFI3 View 3D Structure Click here
B8A403 View 3D Structure Click here
C0HEB4 View 3D Structure Click here
C0HLF1 View 3D Structure Click here
C0PFY3 View 3D Structure Click here
C6SXR3 View 3D Structure Click here
C6SZQ0 View 3D Structure Click here
C6SZU4 View 3D Structure Click here
C6T1J5 View 3D Structure Click here
C6T321 View 3D Structure Click here
D4A8T3 View 3D Structure Click here
D4ADP9 View 3D Structure Click here
E9AH61 View 3D Structure Click here
F1M5X2 View 3D Structure Click here
F1Q997 View 3D Structure Click here
F1QFP1 View 3D Structure Click here
F1R3L9 View 3D Structure Click here
G3V9Y9 View 3D Structure Click here
I1J553 View 3D Structure Click here
I1JC59 View 3D Structure Click here
I1JT85 View 3D Structure Click here
I1KG99 View 3D Structure Click here
I1KPU9 View 3D Structure Click here
I1KXB9 View 3D Structure Click here
I1LJA7 View 3D Structure Click here
I1LQ06 View 3D Structure Click here
I1M5A9 View 3D Structure Click here
I1N1K1 View 3D Structure Click here
K7KRS6 View 3D Structure Click here
K9J6Q2 View 3D Structure Click here
M0RD05 View 3D Structure Click here
O00189 View 3D Structure Click here
O01755 View 3D Structure Click here
O16369 View 3D Structure Click here
O17901 View 3D Structure Click here
O22715 View 3D Structure Click here
O23685 View 3D Structure Click here
O50016 View 3D Structure Click here
O62530 View 3D Structure Click here
O62531 View 3D Structure Click here
O74496 View 3D Structure Click here
O74891 View 3D Structure Click here
O82201 View 3D Structure Click here
O96254 View 3D Structure Click here
P35181 View 3D Structure Click here
P35585 View 3D Structure Click here
P35602 View 3D Structure Click here
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P43621 View 3D Structure Click here
P47064 View 3D Structure Click here
P48444 View 3D Structure Click here
P53600 View 3D Structure Click here
P53676 View 3D Structure Click here
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P53678 View 3D Structure Click here
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P54672 View 3D Structure Click here
P56377 View 3D Structure Click here
P59780 View 3D Structure Click here
P61923 View 3D Structure Click here
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P61966 View 3D Structure Click here
P61967 View 3D Structure Click here
P62743 View 3D Structure Click here
P62744 View 3D Structure Click here
P84091 View 3D Structure Click here
P84092 View 3D Structure Click here
Q00381 View 3D Structure Click here
Q00776 View 3D Structure Click here
Q09236 View 3D Structure Click here
Q09718 View 3D Structure Click here
Q09905 View 3D Structure Click here
Q0JK13 View 3D Structure Click here
Q10CG6 View 3D Structure Click here
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Q19123 View 3D Structure Click here
Q20736 View 3D Structure Click here
Q2PWT8 View 3D Structure Click here
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Q32Q06 View 3D Structure Click here
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Q4E596 View 3D Structure Click here
Q54CA7 View 3D Structure Click here
Q54H39 View 3D Structure Click here
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Q54HS9 View 3D Structure Click here
Q54NZ4 View 3D Structure Click here
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Q553S2 View 3D Structure Click here
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Q59KJ6 View 3D Structure Click here
Q59QC5 View 3D Structure Click here
Q59TV8 View 3D Structure Click here
Q5A006 View 3D Structure Click here
Q5AJY4 View 3D Structure Click here
Q5NA06 View 3D Structure Click here
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Q65XN2 View 3D Structure Click here
Q66H80 View 3D Structure Click here
Q66IE3 View 3D Structure Click here
Q6DGS0 View 3D Structure Click here
Q6DKF5 View 3D Structure Click here
Q6NWK2 View 3D Structure Click here
Q6PEJ2 View 3D Structure Click here
Q6Z844 View 3D Structure Click here
Q6ZKE1 View 3D Structure Click here
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Q7TN05 View 3D Structure Click here
Q7XI39 View 3D Structure Click here
Q7XZG1 View 3D Structure Click here
Q7ZU89 View 3D Structure Click here
Q7ZW27 View 3D Structure Click here
Q7ZW98 View 3D Structure Click here
Q84LG4 View 3D Structure Click here
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Q8BSZ2 View 3D Structure Click here
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Q8T874 View 3D Structure Click here
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Q92572 View 3D Structure Click here
Q940S5 View 3D Structure Click here
Q96CW1 View 3D Structure Click here
Q96PC3 View 3D Structure Click here
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Q9P299 View 3D Structure Click here
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Q9SB50 View 3D Structure Click here
Q9VDC3 View 3D Structure Click here
Q9VV89 View 3D Structure Click here
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Q9W555 View 3D Structure Click here
Q9WVL1 View 3D Structure Click here
Q9WVP1 View 3D Structure Click here
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Q9Y587 View 3D Structure Click here
Q9Y6Q5 View 3D Structure Click here
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