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1  structure 1225  species 0  interactions 1530  sequences 18  architectures

Family: Mago-bind (PF09282)

Summary: Mago binding

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.

Mago binding Provide feedback

Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions [1].

Literature references

  1. Bono F, Ebert J, Unterholzner L, Guttler T, Izaurralde E, Conti E; , EMBO Rep. 2004;5:304-310.: Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex. PUBMED:14968132 EPMC:14968132


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015362

Partner of Y14 and mago (PYM, also known as WIBG) is a key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmarks for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation [ PUBMED:18026120 , PUBMED:19410547 ].

The N-terminal domain of PYM adopts a small globular all-beta-domain structure, with a three-stranded beta-sheet and a contiguous beta-hairpin. It binds to both Mago and Y14 [ PUBMED:14968132 ].

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
(46)
Full
(1530)
Representative proteomes UniProt
(2378)
RP15
(276)
RP35
(674)
RP55
(1115)
RP75
(1564)
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
(46)
Full
(1530)
Representative proteomes UniProt
(2378)
RP15
(276)
RP35
(674)
RP55
(1115)
RP75
(1564)
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
(46)
Full
(1530)
Representative proteomes UniProt
(2378)
RP15
(276)
RP35
(674)
RP55
(1115)
RP75
(1564)
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: pdb_1rk8
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sammut SJ
Number in seed: 46
Number in full: 1530
Average length of the domain: 26.6 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 11.47 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 21.2
Noise cut-off 20.5 20.5
Model length: 27
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Mago-bind 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
A0A044V5I8 View 3D Structure Click here
A0A077ZBI8 View 3D Structure Click here
A0A0D2ET30 View 3D Structure Click here
A0A0K0EKS5 View 3D Structure Click here
A0A0N4UEG6 View 3D Structure Click here
A0A0R0GPD9 View 3D Structure Click here
A0A0R0K4W3 View 3D Structure Click here
A0A175WFA3 View 3D Structure Click here
A0A1C1D0D0 View 3D Structure Click here
A6QPH1 View 3D Structure Click here
B0WII7 View 3D Structure Click here
B1WB17 View 3D Structure Click here
B4FUX7 View 3D Structure Click here
B4NSP6 View 3D Structure Click here
B5XDD3 View 3D Structure Click here
B5XG19 View 3D Structure Click here
B6TLX6 View 3D Structure Click here
C0NSG0 View 3D Structure Click here
C1GRI8 View 3D Structure Click here
D3ZGY1 View 3D Structure Click here
G4V9D4 View 3D Structure Click here
I1KSS4 View 3D Structure Click here
J9E9E6 View 3D Structure Click here
M0RCI6 View 3D Structure Click here
P82804 View 3D Structure Click here
Q10NR2 View 3D Structure Click here
Q16LW2 View 3D Structure Click here
Q22615 View 3D Structure Click here
Q2F5J3 View 3D Structure Click here
Q54R88 View 3D Structure Click here
Q6PH11 View 3D Structure Click here
Q7Q6B5 View 3D Structure Click here
Q8CHP5 View 3D Structure Click here
Q8I5V8 View 3D Structure Click here
Q9BRP8 View 3D Structure Click here
Q9LPZ4 View 3D Structure Click here
Q9USW8 View 3D Structure Click here
U7PIW1 View 3D Structure Click here