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0  structures 113  species 0  interactions 308  sequences 5  architectures

Family: Clusterin (PF01093)

Summary: Clusterin

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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.

Clusterin Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000753

Clusterin (Clu), also known as apolipoprotein J, is a vertebrate glycoprotein [PUBMED:1585460]. Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is proteolytically cleaved into alpha- and beta-subunits and further glycosylated to form mature disulfide-linked heterodimeric secretory CLU (sCLU). sCLU is an 80kDa protein and acts as a molecular chaperone, scavenging denatured proteins outside cells [PUBMED:21505792, PUBMED:19535339]. sCLU possesses nonspecific binding activity to hydrophobic domains of various non-native proteins [PUBMED:12551933], binds to some bacteria and bacterial proteins [PUBMED:11720815], and interacts with different immune molecules [PUBMED:27148688].

A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death. The sCLU protein is cytoprotective and anti-apoptotic, whereas the nCLU protein is pro-apoptotic [PUBMED:21953454, PUBMED:22588555, PUBMED:22025968].

This family also includes clusterin-like protein 1 (CLUL1), which is expressed specifically in cone photoreceptor cells [PUBMED:10675623] and is likely to be necessary for normal cone function [PUBMED:14507903].

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(51)
Full
(308)
Representative proteomes UniProt
(506)
NCBI
(897)
Meta
(0)
RP15
(27)
RP35
(89)
RP55
(196)
RP75
(245)
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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
(51)
Full
(308)
Representative proteomes UniProt
(506)
NCBI
(897)
Meta
(0)
RP15
(27)
RP35
(89)
RP55
(196)
RP75
(245)
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
(51)
Full
(308)
Representative proteomes UniProt
(506)
NCBI
(897)
Meta
(0)
RP15
(27)
RP35
(89)
RP55
(196)
RP75
(245)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 51
Number in full: 308
Average length of the domain: 337.40 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 91.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 28.8
Noise cut-off 22.3 22.5
Model length: 430
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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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