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37  structures 1348  species 0  interactions 4102  sequences 74  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 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
(184)
Full
(4102)
Representative proteomes UniProt
(7100)
RP15
(656)
RP35
(1792)
RP55
(3357)
RP75
(4536)
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HTML View  View           
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
(184)
Full
(4102)
Representative proteomes UniProt
(7100)
RP15
(656)
RP35
(1792)
RP55
(3357)
RP75
(4536)
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
(184)
Full
(4102)
Representative proteomes UniProt
(7100)
RP15
(656)
RP35
(1792)
RP55
(3357)
RP75
(4536)
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_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: 184
Number in full: 4102
Average length of the domain: 110.70 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 40.65 %

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 27.9 27.9
Trusted cut-off 27.9 27.9
Noise cut-off 27.8 27.8
Model length: 120
Family (HMM) version: 17
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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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 37 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
A0A0G2JUZ4 View 3D Structure Click here
A0A0G2K8D6 View 3D Structure Click here
A0A0P0XGG0 View 3D Structure Click here
A0A0R4IBL4 View 3D Structure Click here
A0A0R4ITQ3 View 3D Structure Click here
A0A0U1RRP2 View 3D Structure Click here
A0A1D6HL21 View 3D Structure Click here
A0A1D6IA29 View 3D Structure Click here
A0A1D6IKH7 View 3D Structure Click here
A0A1D6KNV0 View 3D Structure Click here
A0A1Y7VP24 View 3D Structure Click here
A0A2R8QJK6 View 3D Structure Click here
A4IAJ8 View 3D Structure Click here
A4IDY5 View 3D Structure Click here
A7MD57 View 3D Structure Click here
B0G147 View 3D Structure Click here
B4FPX6 View 3D Structure Click here
C4J9Z3 View 3D Structure Click here
C6SXF6 View 3D Structure Click here
C6TJD4 View 3D Structure Click here
F1R4W4 View 3D Structure Click here
F4I181 View 3D Structure Click here
I1KTX6 View 3D Structure Click here
I1L5W9 View 3D Structure Click here
I1LZM2 View 3D Structure Click here
I1MJC8 View 3D Structure Click here
I1MTX5 View 3D Structure Click here
I1N4E2 View 3D Structure Click here
K7UEY2 View 3D Structure Click here
Q12395 View 3D Structure Click here
Q4CTL1 View 3D Structure Click here
Q4D2C3 View 3D Structure Click here
Q4D9X6 View 3D Structure Click here
Q4V8B2 View 3D Structure Click here
Q54GP1 View 3D Structure Click here
Q5ADL9 View 3D Structure Click here
Q5PPL2 View 3D Structure Click here
Q5RHX6 View 3D Structure Click here
Q67UK2 View 3D Structure Click here
Q6PH85 View 3D Structure Click here
Q7X6I9 View 3D Structure Click here
Q86JM4 View 3D Structure Click here
Q8BZJ7 View 3D Structure Click here
Q8CCA0 View 3D Structure Click here
Q8IWE4 View 3D Structure Click here
Q8K0V2 View 3D Structure Click here
Q8T8S1 View 3D Structure Click here
Q8WZK4 View 3D Structure Click here
Q92564 View 3D Structure Click here
Q96GG9 View 3D Structure Click here
Q9BTE7 View 3D Structure Click here
Q9CXV9 View 3D Structure Click here
Q9LTV9 View 3D Structure Click here
Q9MBG8 View 3D Structure Click here
Q9QZ73 View 3D Structure Click here
Q9U3C8 View 3D Structure Click here
Q9VUQ8 View 3D Structure Click here
Q9VWB1 View 3D Structure Click here