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0  structures 48  species 0  interactions 180  sequences 3  architectures

Family: Clusterin (PF01093)

Summary: Clusterin

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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 is a vertebrate glycoprotein [PUBMED:1585460], the exact function of which is not yet clear. 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 further glycosylated and proteolytically cleaved into alpha- and beta-subunits, held together by disulphide bonds. External sCLU is an 80kDa protein and may act as a molecular chaperone, scavenging denatured proteins outside cells following specific stress-induced injury such as heat shock. sCLU possesses nonspecific binding activity to hydrophobic domains of various proteins in vitro [PUBMED:12551933].

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.

Clusterin is synthesized as a precursor polypeptide of about 400 amino acids which is post-translationally cleaved to form two subunits of about 200 amino acids each. The two subunits are linked by five disulphide bonds to form an antiparallel ladder-like structure [PUBMED:1491011]. In each of the mature subunits the five cysteines that are involved in disulphide bonds are clustered in domains of about 30 amino acids located in the central part of the subunits.

This entry represents the clusterin precursor and related 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(14)
Full
(180)
Representative proteomes NCBI
(144)
Meta
(0)
RP15
(4)
RP35
(8)
RP55
(23)
RP75
(59)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(14)
Full
(180)
Representative proteomes NCBI
(144)
Meta
(0)
RP15
(4)
RP35
(8)
RP55
(23)
RP75
(59)
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
(14)
Full
(180)
Representative proteomes NCBI
(144)
Meta
(0)
RP15
(4)
RP35
(8)
RP55
(23)
RP75
(59)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Finn RD, Bateman A
Number in seed: 14
Number in full: 180
Average length of the domain: 339.10 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 92.73 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.3 20.3
Noise cut-off 19.9 18.7
Model length: 436
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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