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53  structures 1763  species 0  interactions 2297  sequences 43  architectures

Family: eIF-6 (PF01912)

Summary: eIF-6 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.

eIF-6 family Provide feedback

This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002769

This family includes eukaryotic translation initiation factor 6 (eIF6) as well as presumed archaeal homologues.

The assembly of 80S ribosomes requires joining of the 40S and 60S subunits, which is triggered by the formation of an initiation complex on the 40S subunit. This event is rate-limiting for translation, and depends on external stimuli and the status of the cell. Eukaryotic translation initiation factor 6 (eIF6) binds specifically to the free 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit ribosomes [ PUBMED:9891075 ]. Furthermore, eIF6 interacts in the cytoplasm with RACK1, a receptor for activated protein kinase C (PKC). RACK1 is a major component of translating ribosomes, which harbour significant amounts of PKC. Loading 60S subunits with eIF6 caused a dose-dependent translational block and impairment of 80S formation, which are reversed by expression of RACK1 and stimulation of PKC in vivo and in vitro. PKC stimulation leads to eIF6 phosphorylation and its release, promoting 80S subunit formation. RACK1 provides a physical and functional link between PKC signalling and ribosome activation [ PUBMED:11238882 , PUBMED:10206977 , PUBMED:9405604 ].

All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function [ PUBMED:11524672 ].

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 GME (CL0197), which has the following description:

This superfamily contains a number of related enzymes such as AstB, peptidyl-arginine deiminase, arginine deiminase and amidinotransferase [1,2].

The clan contains the following 6 members:

ADI AstB DDAH_eukar eIF-6 PAD PAD_porph

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
(132)
Full
(2297)
Representative proteomes UniProt
(5634)
RP15
(512)
RP35
(1138)
RP55
(1862)
RP75
(2565)
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
(132)
Full
(2297)
Representative proteomes UniProt
(5634)
RP15
(512)
RP35
(1138)
RP55
(1862)
RP75
(2565)
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
(132)
Full
(2297)
Representative proteomes UniProt
(5634)
RP15
(512)
RP35
(1138)
RP55
(1862)
RP75
(2565)
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: Enright A
Previous IDs: eIF6;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 132
Number in full: 2297
Average length of the domain: 183.6 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 74.55 %

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 25.0 25.0
Trusted cut-off 25.5 25.0
Noise cut-off 24.8 23.2
Model length: 197
Family (HMM) version: 21
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 eIF-6 domain has been found. There are 53 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
A0A044QT40 View 3D Structure Click here
A0A077Z2N0 View 3D Structure Click here
A0A0D2F9F8 View 3D Structure Click here
A0A0J9Y5A4 View 3D Structure Click here
A0A0K0E913 View 3D Structure Click here
A0A0N4U5Z3 View 3D Structure Click here
A0A0R0FTI5 View 3D Structure Click here
A0A0R0HV63 View 3D Structure Click here
A0A0R0IF42 View 3D Structure Click here
A0A183Y1W6 View 3D Structure Click here
A0A1C1CK46 View 3D Structure Click here
A0A3Q0KV00 View 3D Structure Click here
A0RYC3 View 3D Structure Click here
A1RXF3 View 3D Structure Click here
A2BN57 View 3D Structure Click here
A2STI7 View 3D Structure Click here
A3DNH5 View 3D Structure Click here
A4ICP5 View 3D Structure Click here
A4RSQ6 View 3D Structure Click here
A6UT95 View 3D Structure Click here
A7ANL7 View 3D Structure Click here
A7I9I6 View 3D Structure Click here
A9A305 View 3D Structure Click here
B4FKD5 View 3D Structure Click here
B8GEU6 View 3D Structure Click here
B8MDN4 View 3D Structure Click here
B9PVB9 View 3D Structure Click here
C0NDT9 View 3D Structure Click here
C1H222 View 3D Structure Click here
C9SV08 View 3D Structure Click here
D1ZG64 View 3D Structure Click here
I1L3P5 View 3D Structure Click here
I1MQC8 View 3D Structure Click here
I1NIE5 View 3D Structure Click here
K7LK09 View 3D Structure Click here
O22290 View 3D Structure Click here
O27648 View 3D Structure Click here
O28214 View 3D Structure Click here
O55135 View 3D Structure Click here
O62106 View 3D Structure Click here