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1  structure 59  species 0  interactions 2174  sequences 42  architectures

Family: TTR-52 (PF01060)

Summary: Transthyretin-like family

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.

Transthyretin-like family Provide feedback

TTR-52 was called family 2 in [1] and has weak similarity to transthyretin (formerly called pre-albumin) which transports thyroid hormones. The specific function of this protein is as a bridging molecule in apoptosis cross-linking dying cells to phagocytes. TTR-52 bridges by cross-linking surface-exposed phosphatidylserine (PtdSer) on apoptotic cells to the CED-1 receptor, a transmembrane receptor, on phagocytes. TTR-52 has an open beta-barrel-like structure [2].

Literature references

  1. Sonnhammer EL, Durbin R; , Genomics 1997;46:200-216.: Analysis of protein domain families in Caenorhabditis elegans. PUBMED:9417907 EPMC:9417907

  2. Kang Y, Zhao D, Liang H, Liu B, Zhang Y, Liu Q, Wang X, Liu Y;, Genes Dev. 2012;26:1339-1350.: Structural study of TTR-52 reveals the mechanism by which a bridging molecule mediates apoptotic cell engulfment. PUBMED:22713871 EPMC:22713871


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001534

Transthyretin-related proteins form a nematode-specific expanded protein family that comprises 59 members, 54 of which are predicted to be secreted. The proteins show weak similarity to transthyretin (formerly called prealbumin) which transports thyroid hormones. [ PUBMED:9417907 ]. Some transthyretin-related genes are induced in response to environmental challenges such as oxidative stress or pathogen exposure. These proteins possess 4 cysteine residues that are conserved within the C. elegans transthyretin-related protein family, which could serve as reactive oxygen sensors or scavengers [ PUBMED:29346382 ].

Transthyretin-related protein 52 (TTR-52), a member of this family, is required for efficient cell corpse engulfment by the recognition the surface exposed phosphatidylserine (PS). TTR-52 mediates recognition of apoptotic cells by cross-linking the PS signal with the phagocyte receptor CED-1 [ PUBMED:20526330 ].

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

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
(95)
Full
(2174)
Representative proteomes UniProt
(3465)
RP15
(1188)
RP35
(1535)
RP55
(2011)
RP75
(2173)
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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
(95)
Full
(2174)
Representative proteomes UniProt
(3465)
RP15
(1188)
RP35
(1535)
RP55
(2011)
RP75
(2173)
Alignment:
Format:
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Sequence:
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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
(95)
Full
(2174)
Representative proteomes UniProt
(3465)
RP15
(1188)
RP35
(1535)
RP55
(2011)
RP75
(2173)
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: [1]
Previous IDs: Worm_family_2; DUF290;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 95
Number in full: 2174
Average length of the domain: 78.30 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 46.20 %

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 24.9 24.9
Trusted cut-off 24.9 24.9
Noise cut-off 24.8 24.8
Model length: 81
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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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 TTR-52 domain has been found. There are 1 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
A3FPK9 View 3D Structure Click here
A7DT35 View 3D Structure Click here
A7LPC7 View 3D Structure Click here
A8DZ30 View 3D Structure Click here
A8DZ31 View 3D Structure Click here
G5ED35 View 3D Structure Click here
G5EE48 View 3D Structure Click here
H2KYJ2 View 3D Structure Click here
J7SF92 View 3D Structure Click here
O01517 View 3D Structure Click here
O16586 View 3D Structure Click here
O17345 View 3D Structure Click here
O17635 View 3D Structure Click here
O17776 View 3D Structure Click here
O61977 View 3D Structure Click here
O62289 View 3D Structure Click here
O62448 View 3D Structure Click here
P34499 View 3D Structure Click here
P34500 View 3D Structure Click here
P34502 View 3D Structure Click here
P55955 View 3D Structure Click here
Q03575 View 3D Structure Click here
Q17473 View 3D Structure Click here
Q17629 View 3D Structure Click here
Q17937 View 3D Structure Click here
Q18256 View 3D Structure Click here
Q18878 View 3D Structure Click here
Q19694 View 3D Structure Click here
Q1W0R1 View 3D Structure Click here
Q20089 View 3D Structure Click here
Q22032 View 3D Structure Click here
Q22034 View 3D Structure Click here
Q22035 View 3D Structure Click here
Q22176 View 3D Structure Click here
Q22192 View 3D Structure Click here
Q22285 View 3D Structure Click here
Q22288 View 3D Structure Click here
Q22341 View 3D Structure Click here
Q22499 View 3D Structure Click here
Q22500 View 3D Structure Click here
Q22643 View 3D Structure Click here
Q23378 View 3D Structure Click here
Q2EEM8 View 3D Structure Click here
Q45EK1 View 3D Structure Click here
Q65ZI4 View 3D Structure Click here
Q65ZI5 View 3D Structure Click here
Q7YZH4 View 3D Structure Click here
Q86NH9 View 3D Structure Click here
Q8I7H9 View 3D Structure Click here
Q93805 View 3D Structure Click here
Q93832 View 3D Structure Click here
Q95QW9 View 3D Structure Click here
Q95Y92 View 3D Structure Click here
Q95Y93 View 3D Structure Click here
Q9XV18 View 3D Structure Click here
Q9XWL1 View 3D Structure Click here
Q9XXQ6 View 3D Structure Click here
Q9XXR4 View 3D Structure Click here
Q9XXR5 View 3D Structure Click here
V6CLT2 View 3D Structure Click here