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39  structures 1407  species 0  interactions 4883  sequences 90  architectures

Family: PABP (PF00658)

Summary: Poly-adenylate binding protein, unique 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.

Poly-adenylate binding protein, unique domain Provide feedback

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (PF00076) [1]. Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family.

Literature references

  1. Mangus DA, Evans MC, Jacobson A; , Genome Biol 2003;4:223.: Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. PUBMED:12844354 EPMC:12844354


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002004

The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains ( INTERPRO ) [ PUBMED:11287654 ]. PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [ PUBMED:11940585 ].

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
(127)
Full
(4883)
Representative proteomes UniProt
(8887)
RP15
(784)
RP35
(2189)
RP55
(4110)
RP75
(5454)
Jalview View  View  View  View  View  View  View 
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
(127)
Full
(4883)
Representative proteomes UniProt
(8887)
RP15
(784)
RP35
(2189)
RP55
(4110)
RP75
(5454)
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
(127)
Full
(4883)
Representative proteomes UniProt
(8887)
RP15
(784)
RP35
(2189)
RP55
(4110)
RP75
(5454)
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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 127
Number in full: 4883
Average length of the domain: 65.00 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 7.67 %

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 30.6 30.6
Trusted cut-off 30.6 30.7
Noise cut-off 30.5 30.5
Model length: 66
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 PABP domain has been found. There are 39 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
A0A1D6E6L1 View 3D Structure Click here
A0A1D6ELH4 View 3D Structure Click here
A0A1D6I0G1 View 3D Structure Click here
A0A1D6J9R4 View 3D Structure Click here
A2A5N3 View 3D Structure Click here
A4I150 View 3D Structure Click here
A4IBV3 View 3D Structure Click here
A4IC57 View 3D Structure Click here
B5DF80 View 3D Structure Click here
D3ZAS7 View 3D Structure Click here
D3ZSR2 View 3D Structure Click here
D4A233 View 3D Structure Click here
F1QB54 View 3D Structure Click here
G3V9N0 View 3D Structure Click here
I1JDA2 View 3D Structure Click here
I1JDA5 View 3D Structure Click here
I1JE12 View 3D Structure Click here
I1JPU1 View 3D Structure Click here
I1K813 View 3D Structure Click here
I1KM25 View 3D Structure Click here
I1M8P0 View 3D Structure Click here
I1MP18 View 3D Structure Click here
I1MP19 View 3D Structure Click here
I1MXM6 View 3D Structure Click here
I1NAF8 View 3D Structure Click here
I1NH63 View 3D Structure Click here
K7VF25 View 3D Structure Click here
K7WAC5 View 3D Structure Click here
O22173 View 3D Structure Click here
O64380 View 3D Structure Click here
P04147 View 3D Structure Click here
P11940 View 3D Structure Click here
P21187 View 3D Structure Click here
P29341 View 3D Structure Click here
P31209 View 3D Structure Click here
P42731 View 3D Structure Click here
Q00M91 View 3D Structure Click here
Q05196 View 3D Structure Click here
Q0DB96 View 3D Structure Click here
Q10N87 View 3D Structure Click here
Q13310 View 3D Structure Click here
Q19579 View 3D Structure Click here
Q1ZXC2 View 3D Structure Click here
Q4E4I9 View 3D Structure Click here
Q4E4V0 View 3D Structure Click here
Q4VXU2 View 3D Structure Click here
Q54BM2 View 3D Structure Click here
Q5AI15 View 3D Structure Click here
Q62029 View 3D Structure Click here
Q6P3L1 View 3D Structure Click here
Q6PHQ9 View 3D Structure Click here
Q6TGY6 View 3D Structure Click here
Q6YYV1 View 3D Structure Click here
Q6Z050 View 3D Structure Click here
Q7F8Y1 View 3D Structure Click here
Q7T3G5 View 3D Structure Click here
Q8I5H4 View 3D Structure Click here
Q9D4E6 View 3D Structure Click here
Q9EPH8 View 3D Structure Click here
Q9FXA2 View 3D Structure Click here
Q9H361 View 3D Structure Click here
Q9LT82 View 3D Structure Click here
Q9U302 View 3D Structure Click here
Q9ZQA8 View 3D Structure Click here