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33  structures 981  species 2  interactions 2480  sequences 47  architectures

Family: Cullin_binding (PF03556)

Summary: Cullin binding

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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.

Cullin binding Provide feedback

This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation [1-3]. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices [1,2].

Literature references

  1. Yang X, Zhou J, Sun L, Wei Z, Gao J, Gong W, Xu RM, Rao Z, Liu Y;, J Biol Chem. 2007;282:24490-24494.: Structural basis for the function of DCN-1 in protein Neddylation. PUBMED:17597076 EPMC:17597076

  2. Kurz T, Chou YC, Willems AR, Meyer-Schaller N, Hecht ML, Tyers M, Peter M, Sicheri F;, Mol Cell. 2008;29:23-35.: Dcn1 functions as a scaffold-type E3 ligase for cullin neddylation. PUBMED:18206966 EPMC:18206966

  3. Kim AY, Bommelje CC, Lee BE, Yonekawa Y, Choi L, Morris LG, Huang G, Kaufman A, Ryan RJ, Hao B, Ramanathan Y, Singh B;, J Biol Chem. 2008;283:33211-33220.: SCCRO (DCUN1D1) is an essential component of the E3 complex for neddylation. PUBMED:18826954 EPMC:18826954


This tab holds annotation information from the InterPro database.

InterPro entry IPR005176

This domain is found in the eukaryotic family defective in cullin neddylation, which includes DCN1 and DCN1-like proteins. Proteins of the DCN family may contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes, which are multi-protein complexes required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome [PUBMED:15988528, PUBMED:18826954].

The structure of this domain is composed entirely of alpha helices [PUBMED:17597076, PUBMED:18206966]. It has been referred to as potentiating neddylation domain (PONY) and can be found in association with an N-terminal UBA domain. The PONY domain contains a cullin-binding surface within its C-terminal region and is sufficient to promote neddylation [PUBMED:18206966].

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

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(205)
Full
(2480)
Representative proteomes UniProt
(3537)
NCBI
(4875)
Meta
(5)
RP15
(595)
RP35
(1241)
RP55
(1878)
RP75
(2279)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(205)
Full
(2480)
Representative proteomes UniProt
(3537)
NCBI
(4875)
Meta
(5)
RP15
(595)
RP35
(1241)
RP55
(1878)
RP75
(2279)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(205)
Full
(2480)
Representative proteomes UniProt
(3537)
NCBI
(4875)
Meta
(5)
RP15
(595)
RP35
(1241)
RP55
(1878)
RP75
(2279)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_3021 (release 7.0)
Previous IDs: DUF298;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Mistry J , Wood V , Eberhardt R
Number in seed: 205
Number in full: 2480
Average length of the domain: 111.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 40.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.9 27.9
Trusted cut-off 28.0 28.1
Noise cut-off 27.8 27.6
Model length: 120
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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

Selections

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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...

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Interactions

There are 2 interactions for this family. More...

Cullin_Nedd8 Cullin_binding

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 Cullin_binding domain has been found. There are 33 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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