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68  structures 1468  species 0  interactions 10424  sequences 198  architectures

Family: Adap_comp_sub (PF00928)

Summary: Adaptor complexes medium subunit family

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This is the Wikipedia entry entitled "Adaptor complexes medium subunit domain". More...

Adaptor complexes medium subunit domain Edit Wikipedia article


Adap_comp_sub
PDB 1h6e EBI.jpg
mu2 adaptin subunit (ap50) of ap2 adaptor (second domain), complexed with ctla-4 internalization peptide ttgvyvkmppt
Identifiers
Symbol Adap_comp_sub
Pfam PF00928
Pfam clan CL0448
InterPro IPR008968
PROSITE PDOC00761
SCOP 1bxx
SUPERFAMILY 1bxx

In molecular biology, the adaptor complexes medium subunit domain is a protein domain found at the C-terminus of the mu subunit from various clathrin adaptor protein complexes (AP1, AP2, AP3, AP4 and AP5)[1] and muniscins. The C-terminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors.[2] The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear.[3] The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle.[3]

References

  1. ^ Mattera R, Guardia CM, Sidhu SS, Bonifacino JS (2015). "Bivalent Motif-Ear Interactions Mediate the Association of the Accessory Protein Tepsin with the AP-4 Adaptor Complex". The Journal of Biological Chemistry. 290 (52): 30736–49. doi:10.1074/jbc.M115.683409. PMC 4692204Freely accessible. PMID 26542808. 
  2. ^ Follows ER, McPheat JC, Minshull C, Moore NC, Pauptit RA, Rowsell S, Stacey CL, Stanway JJ, Taylor IW, Abbott WM (October 2001). "Study of the interaction of the medium chain mu 2 subunit of the clathrin-associated adapter protein complex 2 with cytotoxic T-lymphocyte antigen 4 and CD28". Biochem. J. 359 (Pt 2): 427–34. doi:10.1042/0264-6021:3590427. PMC 1222163Freely accessible. PMID 11583591. 
  3. ^ a b Nakayama Y, Goebl M, O'Brine Greco B, Lemmon S, Pingchang Chow E, Kirchhausen T (December 1991). "The medium chains of the mammalian clathrin-associated proteins have a homolog in yeast". Eur. J. Biochem. 202 (2): 569–74. doi:10.1111/j.1432-1033.1991.tb16409.x. PMID 1761056. 


External links

This article incorporates text from the public domain Pfam and InterPro IPR008968

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.

Adaptor complexes medium subunit family Provide feedback

This family also contains members which are coatomer subunits.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR028565

The mu homology domain (MHD) is an ~280 residue protein-protein interaction module, which is found in endocytotic proteins involved in clathrin-mediated endocytosis [ PUBMED:11381094 , PUBMED:11454741 , PUBMED:14726597 , PUBMED:19713939 ]:

  • Mu subunits of adaptor protein (AP) complexes, AP-1, AP-2, AP-3, and AP-4.
  • Proteins of the stonin family.
  • Proteins of the muniscin family: Syp1, FCHO1/2 and SGIP1.

The MHD domain has an elongated, banana-shaped, all beta-sheet structure. It can be considered as two beta-sandwich subdomains (A and B), with subdomain B inserted between strands 6 and 15 of subdomain A, and joined edge to edge such that the convex surface is a continuous nine-stranded mixed beta-sheet that runs the whole length of the molecule. The tyrosine based signal binds to a site on the surface of two parallel beta-sheet strands (beta1 and beta16) in subdomain A [ PUBMED:19713939 , PUBMED:9812899 ].

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 Cargo_bd_muHD (CL0448), which has the following description:

Internalisation of diverse transmembrane cargos from the plasma membrane requires a similarly diverse array of specialized adaptors, this domain is the binding domain of these endocytioc adaptors. The muHD binds directly to the cytosolic tail of the Mid2 (for the transmembrane stress sensor protein Mid2) cargo protein and mediates Mid2 internalization [1]. These are all-beta proteins.

The clan contains the following 2 members:

Adap_comp_sub muHD

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
(46)
Full
(10424)
Representative proteomes UniProt
(19526)
RP15
(1924)
RP35
(4685)
RP55
(8338)
RP75
(11068)
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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
(46)
Full
(10424)
Representative proteomes UniProt
(19526)
RP15
(1924)
RP35
(4685)
RP55
(8338)
RP75
(11068)
Alignment:
Format:
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Sequence:
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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
(46)
Full
(10424)
Representative proteomes UniProt
(19526)
RP15
(1924)
RP35
(4685)
RP55
(8338)
RP75
(11068)
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: Pfam-B_1007 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Coggill P
Number in seed: 46
Number in full: 10424
Average length of the domain: 258.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 53.33 %

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 31.6 31.6
Trusted cut-off 31.7 31.6
Noise cut-off 31.5 31.5
Model length: 264
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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 Adap_comp_sub domain has been found. There are 68 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
A0A0R0GNH6 View 3D Structure Click here
A0A0R0JB42 View 3D Structure Click here
A0A0R0LIL3 View 3D Structure Click here
A0A0R4IRS1 View 3D Structure Click here
A0A0R4J654 View 3D Structure Click here
A0A1D6DZC7 View 3D Structure Click here
A0A1D6DZC7 View 3D Structure Click here
A0A1D6E563 View 3D Structure Click here
A0A1D6E563 View 3D Structure Click here
A0A1D6EVT1 View 3D Structure Click here
A0A1D6HGI4 View 3D Structure Click here
A0A1D6I9Z4 View 3D Structure Click here
A0A1D6IWX2 View 3D Structure Click here
A0A1D6LL31 View 3D Structure Click here
A0A1D6NJZ7 View 3D Structure Click here
A0A1D6QUI4 View 3D Structure Click here
A0A1D8PG39 View 3D Structure Click here
A0A1D8PND9 View 3D Structure Click here
A2CG10 View 3D Structure Click here
A4HX15 View 3D Structure Click here
A4HZY5 View 3D Structure Click here
A4IA35 View 3D Structure Click here
A4ID91 View 3D Structure Click here
A9JRS9 View 3D Structure Click here
B4FQ20 View 3D Structure Click here
C0PFY3 View 3D Structure Click here
C4IZU7 View 3D Structure Click here
D4AB66 View 3D Structure Click here
F1MAC6 View 3D Structure Click here
F1Q5F9 View 3D Structure Click here
F1Q997 View 3D Structure Click here
F1QDL6 View 3D Structure Click here
F1R3L9 View 3D Structure Click here
F1R8F7 View 3D Structure Click here
F4I562 View 3D Structure Click here
I1J553 View 3D Structure Click here
I1J9J7 View 3D Structure Click here
I1JC59 View 3D Structure Click here
I1JT85 View 3D Structure Click here
I1K2J5 View 3D Structure Click here
I1KXB9 View 3D Structure Click here
I1LF06 View 3D Structure Click here
I1LH11 View 3D Structure Click here
I1LJA7 View 3D Structure Click here
I1LQ06 View 3D Structure Click here
I1MRB2 View 3D Structure Click here
I1MVE9 View 3D Structure Click here
I1N1K1 View 3D Structure Click here
I1NBQ2 View 3D Structure Click here
K7K9X0 View 3D Structure Click here
K7K9X0 View 3D Structure Click here
K7KGJ8 View 3D Structure Click here
K7LJF6 View 3D Structure Click here
K7TSK4 View 3D Structure Click here
O00189 View 3D Structure Click here
O01755 View 3D Structure Click here
O22715 View 3D Structure Click here
O23140 View 3D Structure Click here
O62530 View 3D Structure Click here
O62531 View 3D Structure Click here
O76928 View 3D Structure Click here
O94669 View 3D Structure Click here
P35585 View 3D Structure Click here
P35602 View 3D Structure Click here
P35603 View 3D Structure Click here
P38153 View 3D Structure Click here
P38700 View 3D Structure Click here
P48444 View 3D Structure Click here
P49661 View 3D Structure Click here
P53676 View 3D Structure Click here
P53677 View 3D Structure Click here
P53678 View 3D Structure Click here
P54672 View 3D Structure Click here
P84091 View 3D Structure Click here
P84092 View 3D Structure Click here
P90761 View 3D Structure Click here
Q00776 View 3D Structure Click here
Q09236 View 3D Structure Click here
Q09718 View 3D Structure Click here
Q0DJ99 View 3D Structure Click here
Q0DJA0 View 3D Structure Click here
Q0J649 View 3D Structure Click here
Q0JK13 View 3D Structure Click here
Q20736 View 3D Structure Click here
Q24212 View 3D Structure Click here
Q2PWT8 View 3D Structure Click here
Q32Q06 View 3D Structure Click here
Q499N2 View 3D Structure Click here
Q4CV87 View 3D Structure Click here
Q4DFQ1 View 3D Structure Click here
Q4DGF5 View 3D Structure Click here
Q4DPV5 View 3D Structure Click here
Q4DQU4 View 3D Structure Click here
Q4DVC7 View 3D Structure Click here
Q4DX10 View 3D Structure Click here
Q4DZV1 View 3D Structure Click here
Q54HS9 View 3D Structure Click here
Q54NP5 View 3D Structure Click here
Q55EZ6 View 3D Structure Click here
Q59RK0 View 3D Structure Click here
Q5A2L1 View 3D Structure Click here
Q5AJY4 View 3D Structure Click here
Q5XJY5 View 3D Structure Click here
Q65XN2 View 3D Structure Click here
Q66H80 View 3D Structure Click here
Q6AV18 View 3D Structure Click here
Q6NWK2 View 3D Structure Click here
Q6ZGX8 View 3D Structure Click here
Q7SZZ7 View 3D Structure Click here
Q7XI39 View 3D Structure Click here
Q7ZU89 View 3D Structure Click here
Q7ZW27 View 3D Structure Click here
Q7ZW98 View 3D Structure Click here
Q8BJ63 View 3D Structure Click here
Q8BZ60 View 3D Structure Click here
Q8CDJ8 View 3D Structure Click here
Q8I5M5 View 3D Structure Click here
Q8IEK4 View 3D Structure Click here
Q8IIH2 View 3D Structure Click here
Q8IL63 View 3D Structure Click here
Q8IL63 View 3D Structure Click here
Q8R2R9 View 3D Structure Click here
Q8W0Z6 View 3D Structure Click here
Q8WXE9 View 3D Structure Click here
Q93Y22 View 3D Structure Click here
Q96CW1 View 3D Structure Click here
Q99186 View 3D Structure Click here
Q9BXS5 View 3D Structure Click here
Q9GPF0 View 3D Structure Click here
Q9GPF1 View 3D Structure Click here
Q9H0R1 View 3D Structure Click here
Q9HFE5 View 3D Structure Click here
Q9JKC7 View 3D Structure Click here
Q9JKC8 View 3D Structure Click here
Q9M640 View 3D Structure Click here
Q9SAC9 View 3D Structure Click here
Q9SB50 View 3D Structure Click here
Q9W555 View 3D Structure Click here
Q9WVP1 View 3D Structure Click here
Q9Y2T2 View 3D Structure Click here
Q9Y6Q2 View 3D Structure Click here
Q9Y6Q5 View 3D Structure Click here