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121  structures 1511  species 0  interactions 5077  sequences 94  architectures

Family: Skp1 (PF01466)

Summary: Skp1 family, dimerisation domain

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.

Skp1 family, dimerisation domain Provide feedback

No Pfam abstract.

Literature references

  1. Stebbins CE, Kaelin WG Jr, Pavletich NP; , Science 1999;284:455-461.: Structure of the VHL-ElonginC-ElonginB Complex: Implications for VHL Tumor Suppressor Function. PUBMED:10205047 EPMC:10205047


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016072

SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex [ PUBMED:10205047 ]. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [ PUBMED:8670864 ] and is also involved in the ubiquitin pathway [ PUBMED:9390558 ]. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 [ PUBMED:7852383 ].

This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [ PUBMED:11099048 ], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 [ PUBMED:12553912 ]. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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
(188)
Full
(5077)
Representative proteomes UniProt
(7783)
RP15
(1033)
RP35
(2575)
RP55
(4224)
RP75
(5389)
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
(188)
Full
(5077)
Representative proteomes UniProt
(7783)
RP15
(1033)
RP35
(2575)
RP55
(4224)
RP75
(5389)
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
(188)
Full
(5077)
Representative proteomes UniProt
(7783)
RP15
(1033)
RP35
(2575)
RP55
(4224)
RP75
(5389)
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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 188
Number in full: 5077
Average length of the domain: 46.30 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 23.18 %

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 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.1
Model length: 48
Family (HMM) version: 22
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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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 Skp1 domain has been found. There are 121 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
A0A096UBK9 View 3D Structure Click here
A0A0P0VS32 View 3D Structure Click here
A0A0P0X2H5 View 3D Structure Click here
A0A0P0X908 View 3D Structure Click here
A0A0P0XN22 View 3D Structure Click here
A0A0P0YC82 View 3D Structure Click here
A0A0R0FC80 View 3D Structure Click here
A0A0R0HGK0 View 3D Structure Click here
A0A0R0HM17 View 3D Structure Click here
A0A0R0IBT3 View 3D Structure Click here
A0A0R0LC97 View 3D Structure Click here
A0A1D6F223 View 3D Structure Click here
A0A1D6F7C0 View 3D Structure Click here
A0A1D6F7C1 View 3D Structure Click here
A0A1D6F7U9 View 3D Structure Click here
A0A1D6IPT2 View 3D Structure Click here
A0A1D6IYQ0 View 3D Structure Click here
A0A1D6JJ71 View 3D Structure Click here
A0A1D6JK98 View 3D Structure Click here
A0A1D6N622 View 3D Structure Click here
A0A1D6PM10 View 3D Structure Click here
A0A1D6PU28 View 3D Structure Click here
A3BMD4 View 3D Structure Click here
A4HV28 View 3D Structure Click here
A8MQG7 View 3D Structure Click here
B4FST4 View 3D Structure Click here
C6SZH2 View 3D Structure Click here
C6TH23 View 3D Structure Click here
G5ECU1 View 3D Structure Click here
G5ECY4 View 3D Structure Click here
G5EDD8 View 3D Structure Click here
G5EDY3 View 3D Structure Click here
G5EE67 View 3D Structure Click here
G5EE88 View 3D Structure Click here
G5EE98 View 3D Structure Click here
G5EEX4 View 3D Structure Click here
G5EFA9 View 3D Structure Click here
G5EG39 View 3D Structure Click here
G5EGD5 View 3D Structure Click here
G5EGN7 View 3D Structure Click here