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7  structures 498  species 0  interactions 1643  sequences 22  architectures

Family: Prefoldin_2 (PF01920)

Summary: Prefoldin subunit

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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.

Prefoldin subunit Provide feedback

This family includes prefoldin subunits that are not detected by PF02996.

Literature references

  1. Ha H, Abe K, Artzt K; , Gene 1991;107:345-346.: Primary structure of the embryo-expressed gene KE2 from the mouse H-2K region. PUBMED:1748305 EPMC:1748305

  2. Shang HS, Wong SM, Tan HM, Wu M; , Gene 1994;151:197-201.: YKE2, a yeast nuclear gene encoding a protein showing homology to mouse KE2 and containing a putative leucine-zipper motif. PUBMED:7828874 EPMC:7828874

  3. Geissler S, Siegers K, Schiebel E; , EMBO J 1998;17:952-966.: A novel protein complex promoting formation of functional alpha- and gamma-tubulin. PUBMED:9463374 EPMC:9463374


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002777

Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [PUBMED:11106732, PUBMED:12456645]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6.

Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.

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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Pfam Clan

This family is a member of clan Prefoldin (CL0200), which has the following description:

The Prefoldin domain forms a coiled-coil structure that is involved in substrate-binding in the the chaperone co-factor prefoldin (PFD). Each PFD is assembled from two alpha and four beta subunits. Each alpha subunit contains two, and each beta subunit one, central beta-hairpin that is flanked N- and C-terminally by coiled-coil helices. The N-terminal regions, the prefoldin domain, are found facing into the central cavity of the chaperone. Here exposed hydrophobic patches form an interaction with the substrate (an unfolded protein) [1].

The clan contains the following 3 members:

Prefoldin Prefoldin_2 Prefoldin_3

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...

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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
(56)
Full
(1643)
Representative proteomes NCBI
(1563)
Meta
(97)
RP15
(356)
RP35
(593)
RP55
(877)
RP75
(1100)
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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
(56)
Full
(1643)
Representative proteomes NCBI
(1563)
Meta
(97)
RP15
(356)
RP35
(593)
RP55
(877)
RP75
(1100)
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
(56)
Full
(1643)
Representative proteomes NCBI
(1563)
Meta
(97)
RP15
(356)
RP35
(593)
RP55
(877)
RP75
(1100)
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.

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: Enright A
Previous IDs: KE2;
Type: Family
Author: Enright A, Ouzounis C, Bateman A, Finn RD
Number in seed: 56
Number in full: 1643
Average length of the domain: 102.30 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 68.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 106
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 Prefoldin_2 domain has been found. There are 7 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 seqence.

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