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0  structures 1236  species 0  interactions 3090  sequences 168  architectures

Family: eIF3_p135 (PF12807)

Summary: Translation initiation factor eIF3 subunit 135

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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.

Translation initiation factor eIF3 subunit 135 Provide feedback

Translation initiation factor eIF3 is a multi-subunit protein complex required for initiation of protein biosynthesis in eukaryotic cells. The complex promotes ribosome dissociation, the binding of the initiator methionyl-tRNA to the 40 S ribosomal subunit, and mRNA recruitment to the ribosome. The protein product from TIF31 genes in yeast is p135 which associates with the eIF3 but does not seem to be necessary for protein translation initiation [1].

Literature references

  1. Vornlocher HP, Hanachi P, Ribeiro S, Hershey JW;, J Biol Chem. 1999;274:16802-16812.: A 110-kilodalton subunit of translation initiation factor eIF3 and an associated 135-kilodalton protein are encoded by the Saccharomyces cerevisiae TIF32 and TIF31 genes. PUBMED:10358023 EPMC:10358023


This tab holds annotation information from the InterPro database.

InterPro entry IPR033646

Mutations in the mitochondrial CLU proteins have been shown to result in clustered mitochondria [ PUBMED:12952081 , PUBMED:9207087 , PUBMED:9601101 ]. CLU proteins include Saccharomyces cerevisiae clustered mitochondria protein (Clu1p, alias translation initiation factor 31/TIF31p), Dictyostelium discoideum clustered mitochondria protein homologue (CluA), Caenorhabditis elegans clustered mitochondria protein homologue (CLUH/ Protein KIAA0664), Drosophila clueless (alias clustered mitochondria protein homologue), Arabidopsis clustered mitochondria protein (CLU, alias friendly mitochondria protein/FMT), and human clustered mitochondria protein homologue (CLUH).

Dictyostelium CluA is involved in mitochondrial dynamics and is necessary for both, mitochondrial fission and fusion [ PUBMED:22980139 ]. Drosophila clueless is essential for cytoplasmic localization and function of cellular mitochondria [ PUBMED:23342118 ]. The Drosophila clu gene interacts genetically with parkin (park, the Drosophila ortholog of a human gene responsible for many familial cases of Parkinson's disease) [ PUBMED:19638420 ]. Arabidopsis CLU/FMT is required for correct mitochondrial distribution and morphology [ PUBMED:14617080 ]. The specific role CLU proteins play in mitochondrial processes in not yet known. In an early study, S. cerevisiae Clu1/TIF31p was reported as sometimes being associated with the elF3 translation initiation factor. The authors noted, however, that its tentative assignment as a subunit of elf3 was uncertain, and to date there has been no direct evidence for a role of this protein in translation [ PUBMED:10358023 ].

This entry represents a central domain in CLU proteins.

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...

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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
(139)
Full
(3090)
Representative proteomes UniProt
(5220)
RP15
(512)
RP35
(1490)
RP55
(2535)
RP75
(3320)
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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
(139)
Full
(3090)
Representative proteomes UniProt
(5220)
RP15
(512)
RP35
(1490)
RP55
(2535)
RP75
(3320)
Alignment:
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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
(139)
Full
(3090)
Representative proteomes UniProt
(5220)
RP15
(512)
RP35
(1490)
RP55
(2535)
RP75
(3320)
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: Pfam-B_2213
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Coggill P
Number in seed: 139
Number in full: 3090
Average length of the domain: 156.70 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 11.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 172
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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
A0A0U1RRV5 View 3D Structure Click here
A0A1D6DW96 View 3D Structure Click here
A0A1D6HIA8 View 3D Structure Click here
A0A1D6HN31 View 3D Structure Click here
A0A1D6HXX3 View 3D Structure Click here
A0A1D6JFQ5 View 3D Structure Click here
A0A1D6Q8M9 View 3D Structure Click here
A0A2R8QHY0 View 3D Structure Click here
A0JMD0 View 3D Structure Click here
A1ZAB5 View 3D Structure Click here
A4I7X1 View 3D Structure Click here
E7FE02 View 3D Structure Click here
F4HS99 View 3D Structure Click here
F4HZK4 View 3D Structure Click here
F4J5S1 View 3D Structure Click here
F4JKH6 View 3D Structure Click here
I1JWD6 View 3D Structure Click here
I1KDG4 View 3D Structure Click here
I1KTK7 View 3D Structure Click here
I1MJM1 View 3D Structure Click here
K7KZC4 View 3D Structure Click here
K7KZV0 View 3D Structure Click here
K7L7Y2 View 3D Structure Click here
K7MEU2 View 3D Structure Click here
O15818 View 3D Structure Click here
O59742 View 3D Structure Click here
O75153 View 3D Structure Click here
P34466 View 3D Structure Click here
Q03690 View 3D Structure Click here
Q4D8I4 View 3D Structure Click here
Q4DEY9 View 3D Structure Click here
Q4DJU9 View 3D Structure Click here
Q54KJ2 View 3D Structure Click here
Q54XJ7 View 3D Structure Click here
Q54YP3 View 3D Structure Click here
Q54ZA9 View 3D Structure Click here
Q54ZX7 View 3D Structure Click here
Q59MA9 View 3D Structure Click here
Q5SW19 View 3D Structure Click here
Q6ZGV8 View 3D Structure Click here
Q75JJ2 View 3D Structure Click here
Q75JJ3 View 3D Structure Click here
Q75JR6 View 3D Structure Click here
Q7XQE6 View 3D Structure Click here
Q8IEH7 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;