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12  structures 538  species 0  interactions 4524  sequences 75  architectures

Family: PAM2 (PF07145)

Summary: Ataxin-2 C-terminal region

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.

Ataxin-2 C-terminal region Provide feedback

The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for PF00658. It has been found in a wide range of eukaryotic proteins [1]. Strikingly, this motif appears to occur solely outside of globular domains [1].

Literature references

  1. Albrecht M, Lengauer T; , Biochem Biophys Res Commun 2004;316:129-138.: Survey on the PABC recognition motif PAM2. PUBMED:15003521 EPMC:15003521


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009818

This entry represents a conserved region approximately 250 residues long located towards the C terminus of eukaryotic ataxin-2. Ataxin-2 is a protein of unknown function, within which expansion of a polyglutamine tract (due to expansion of unstable CAG repeats in the coding region of the SCA2 gene) causes spinocerebellar ataxia type 2 (SCA2), a late-onset neurodegenerative disorder [ PUBMED:9339681 ]. The expanded polyglutamine repeat in ataxin-2 causes disruption of the normal morphology of the Golgi complex and increased incidence of cell death [ PUBMED:12812977 ]. Ataxin-2 is predicted to consist of mostly non-globular domains [ PUBMED:9462862 ].

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
(34)
Full
(4524)
Representative proteomes UniProt
(7446)
RP15
(429)
RP35
(1731)
RP55
(3677)
RP75
(5206)
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
(34)
Full
(4524)
Representative proteomes UniProt
(7446)
RP15
(429)
RP35
(1731)
RP55
(3677)
RP75
(5206)
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
(34)
Full
(4524)
Representative proteomes UniProt
(7446)
RP15
(429)
RP35
(1731)
RP55
(3677)
RP75
(5206)
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: Ataxin-2; Ataxin-2_C;
Type: Motif
Sequence Ontology: SO:0001067
Author: Albrecht M , Studholme DJ , Vella Briffa B
Number in seed: 34
Number in full: 4524
Average length of the domain: 17.40 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 3.25 %

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 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 18
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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 PAM2 domain has been found. There are 12 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
A0A096MJE3 View 3D Structure Click here
A0A0G2JVP5 View 3D Structure Click here
A0A0G2JYE0 View 3D Structure Click here
A0A0P0VEA8 View 3D Structure Click here
A0A0P0VQF3 View 3D Structure Click here
A0A1D6F563 View 3D Structure Click here
A0A1D6H885 View 3D Structure Click here
A0A1D6IX46 View 3D Structure Click here
A0A1D6LUI6 View 3D Structure Click here
A0A1D6P125 View 3D Structure Click here
A0A1D6PIX7 View 3D Structure Click here
A0A1D6QMZ5 View 3D Structure Click here
A0A1D6QPS5 View 3D Structure Click here
A0A2R8QJK9 View 3D Structure Click here
A0A2R8RZF5 View 3D Structure Click here
A2CF31 View 3D Structure Click here
B4FZ16 View 3D Structure Click here
B6TAN7 View 3D Structure Click here
B8A588 View 3D Structure Click here
B9G2U1 View 3D Structure Click here
C0P8G0 View 3D Structure Click here
C0PDT1 View 3D Structure Click here
C4J1R7 View 3D Structure Click here
C6TDF4 View 3D Structure Click here
D4AAB9 View 3D Structure Click here
F1M049 View 3D Structure Click here
F1QA42 View 3D Structure Click here
I1JEX4 View 3D Structure Click here
I1JYJ4 View 3D Structure Click here
I1JYJ5 View 3D Structure Click here
I1KB01 View 3D Structure Click here
I1KB03 View 3D Structure Click here
I1KLX1 View 3D Structure Click here
I1M589 View 3D Structure Click here
I1MD33 View 3D Structure Click here
I1MJ23 View 3D Structure Click here
M0R9I5 View 3D Structure Click here
O70305 View 3D Structure Click here
P52479 View 3D Structure Click here
Q09779 View 3D Structure Click here
Q10QX0 View 3D Structure Click here
Q14106 View 3D Structure Click here
Q14106 View 3D Structure Click here
Q14694 View 3D Structure Click here
Q149F3 View 3D Structure Click here
Q3KR59 View 3D Structure Click here
Q55DE7 View 3D Structure Click here
Q5QNG0 View 3D Structure Click here
Q5U4F2 View 3D Structure Click here
Q5U4F2 View 3D Structure Click here
Q5Z8U9 View 3D Structure Click here
Q69K57 View 3D Structure Click here
Q69UJ1 View 3D Structure Click here
Q6AXZ0 View 3D Structure Click here
Q6AYD5 View 3D Structure Click here
Q6ESU4 View 3D Structure Click here
Q7TQH0 View 3D Structure Click here
Q86IW7 View 3D Structure Click here
Q8IYD1 View 3D Structure Click here
Q8L793 View 3D Structure Click here
Q8R050 View 3D Structure Click here
Q8VE62 View 3D Structure Click here
Q8WWM7 View 3D Structure Click here
Q91W45 View 3D Structure Click here
Q94AM9 View 3D Structure Click here
Q99700 View 3D Structure Click here
Q9BPZ3 View 3D Structure Click here
Q9C8M0 View 3D Structure Click here
Q9D6V8 View 3D Structure Click here
Q9FGE6 View 3D Structure Click here
Q9H074 View 3D Structure Click here
Q9JM55 View 3D Structure Click here
Q9JM55 View 3D Structure Click here
Q9LHL3 View 3D Structure Click here
Q9LPI5 View 3D Structure Click here
Q9LRR6 View 3D Structure Click here
Q9S7N9 View 3D Structure Click here
Q9SG10 View 3D Structure Click here
Q9ULR5 View 3D Structure Click here
Q9VG13 View 3D Structure Click here
Q9VJF5 View 3D Structure Click here
Q9VJF6 View 3D Structure Click here
Q9VK85 View 3D Structure Click here
Q9VM05 View 3D Structure Click here