Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
21  structures 481  species 0  interactions 11995  sequences 301  architectures

Family: SOCS_box (PF07525)

Summary: SOCS box

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

SOCS box Provide feedback

The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.

Literature references

  1. Kile BT, Schulman BA, Alexander WS, Nicola NA, Martin HM, Hilton DJ; , Trends Biochem Sci 2002;27:235-241.: The SOCS box: a tale of destruction and degradation. PUBMED:12076535 EPMC:12076535


This tab holds annotation information from the InterPro database.

InterPro entry IPR001496

The SOCS box was first identified in SH2-domain-containing proteins of the suppressor of cytokines signalling (SOCS) family [ PUBMED:9202125 ] but was later also found in:

  • the WSB (WD-40-repeat-containing proteins with a SOCS box) family,
  • the SSB (SPRY domain-containing proteins with a SOCS box) family,
  • the ASB (ankyrin-repeat-containing proteins with a SOCS box) family,
  • and ras and ras-like GTPases [ PUBMED:9419338 ].

The SOCS box found in these proteins is an about 50 amino acid C-terminal domain composed of two blocks of well-conserved residues separated by between 2 and 10 non-conserved residues [ PUBMED:9419338 ]. The C-terminal conserved region is an L/P-rich sequence of unknown function, whereas the N-terminal conserved region is a consensus BC box [ PUBMED:9869640 ], which binds to the Elongin BC complex [ PUBMED:9869640 , PUBMED:10051596 ]. It has been demonstrated that this association couple bound proteins to the ubiquitination or proteasomal compartments [ PUBMED:10051596 , PUBMED:15601820 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan SOCS_box (CL0642), which has the following description:

This superfamily includes the SOCS-box domain and the VHL-box domain [1].

The clan contains the following 2 members:

SOCS_box VHL_C

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...

View options

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
(365)
Full
(11995)
Representative proteomes UniProt
(22121)
RP15
(1762)
RP35
(4010)
RP55
(9239)
RP75
(12413)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(365)
Full
(11995)
Representative proteomes UniProt
(22121)
RP15
(1762)
RP35
(4010)
RP55
(9239)
RP75
(12413)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(365)
Full
(11995)
Representative proteomes UniProt
(22121)
RP15
(1762)
RP35
(4010)
RP55
(9239)
RP75
(12413)
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: [1]
Previous IDs: Clip; SOCS_Clip;
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 365
Number in full: 11995
Average length of the domain: 38.1 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 9.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.4 23.4
Model length: 38
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 SOCS_box domain has been found. There are 21 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.

Loading structure mapping...

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
A0A044QT90 View 3D Structure Click here
A0A044RME0 View 3D Structure Click here
A0A044RME6 View 3D Structure Click here
A0A044TR31 View 3D Structure Click here
A0A044UDR4 View 3D Structure Click here
A0A077YYA1 View 3D Structure Click here
A0A077Z407 View 3D Structure Click here
A0A077ZLV2 View 3D Structure Click here
A0A0G2JZ15 View 3D Structure Click here
A0A0G2K9S1 View 3D Structure Click here
A0A0J9Y9M5 View 3D Structure Click here
A0A0K0E1I5 View 3D Structure Click here
A0A0K0E2S4 View 3D Structure Click here
A0A0K0E757 View 3D Structure Click here
A0A0N4U197 View 3D Structure Click here
A0A0N4U998 View 3D Structure Click here
A0A0N4UF72 View 3D Structure Click here
A0A0R4IA11 View 3D Structure Click here
A0A0R4IAA4 View 3D Structure Click here
A0A0R4IFZ8 View 3D Structure Click here
A0A0R4IHQ5 View 3D Structure Click here
A0A140LGI6 View 3D Structure Click here
A0A1P6C0A0 View 3D Structure Click here
A0A286Y9U7 View 3D Structure Click here
A0A2K6VKJ7 View 3D Structure Click here
A0A2K6VLC7 View 3D Structure Click here
A0A2K6VLH9 View 3D Structure Click here
A0A2R8PZ70 View 3D Structure Click here
A0A2R8Q1K5 View 3D Structure Click here
A0A2R8Q6H6 View 3D Structure Click here
A0A2R8RQU2 View 3D Structure Click here
A0A3P7DCI0 View 3D Structure Click here
A0A3P7DR47 View 3D Structure Click here
A0A3P7ER69 View 3D Structure Click here
A0A3P7FEQ3 View 3D Structure Click here
A0A3Q0KNI3 View 3D Structure Click here
A0A5K4F235 View 3D Structure Click here
A0A5K4F3F7 View 3D Structure Click here
A0A5K4F4Z3 View 3D Structure Click here
A1Z6E0 View 3D Structure Click here