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0  structures 1287  species 0  interactions 2544  sequences 170  architectures

Family: CLU (PF13236)

Summary: Clustered mitochondria

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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.

Clustered mitochondria Provide feedback

The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport [1,2] although the exact function of the domain is unknown [4]. In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane [2] suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast [1]. Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre [1]. It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure [3].

Literature references

  1. Zhu Q, Hulen D, Liu T, Clarke M;, Proc Natl Acad Sci U S A. 1997;94:7308-7313.: The cluA- mutant of Dictyostelium identifies a novel class of proteins required for dispersion of mitochondria. PUBMED:9207087 EPMC:9207087

  2. Fields SD, Arana Q, Heuser J, Clarke M;, J Muscle Res Cell Motil. 2002;23:829-838.: Mitochondrial membrane dynamics are altered in cluA- mutants of Dictyostelium. PUBMED:12952081 EPMC:12952081

  3. Cox RT, Spradling AC;, Dis Model Mech. 2009;2:490-499.: Clueless, a conserved Drosophila gene required for mitochondrial subcellular localization, interacts genetically with parkin. PUBMED:19638420 EPMC:19638420

  4. Sugden C, Ross S, Bloomfield G, Ivens A, Skelton J, Mueller-Taubenberger A, Williams JG;, J Biol Chem. 2010;285:22927-22935.: Two novel Src homology 2 domain proteins interact to regulate dictyostelium gene expression during growth and early development. PUBMED:20457612 EPMC:20457612


This tab holds annotation information from the InterPro database.

InterPro entry IPR025697

The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in highly conserved eukaryotic proteins required for correct mitochondrial dispersal [ PUBMED:9207087 , PUBMED:12952081 ]. The exact function of the domain is unknown [ PUBMED:20457612 ].

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
(109)
Full
(2544)
Representative proteomes UniProt
(3805)
RP15
(506)
RP35
(1121)
RP55
(1948)
RP75
(2577)
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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
(109)
Full
(2544)
Representative proteomes UniProt
(3805)
RP15
(506)
RP35
(1121)
RP55
(1948)
RP75
(2577)
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
(109)
Full
(2544)
Representative proteomes UniProt
(3805)
RP15
(506)
RP35
(1121)
RP55
(1948)
RP75
(2577)
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: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Fey P, Coggill P
Number in seed: 109
Number in full: 2544
Average length of the domain: 222.20 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 17.45 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 225
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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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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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
A0A0R0E7C2 View 3D Structure Click here
A0A0R0KJN5 View 3D Structure Click here
A0A0U1RRV5 View 3D Structure Click here
A0A1D6EBE6 View 3D Structure Click here
A0A1D6HIA8 View 3D Structure Click here
A0A1D6IXA4 View 3D Structure Click here
A0A1D6P7F7 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
A4HX63 View 3D Structure Click here
A4I7X1 View 3D Structure Click here
E7FE02 View 3D Structure Click here
F4J5S1 View 3D Structure Click here
I1KTK7 View 3D Structure Click here
I1MJM1 View 3D Structure Click here
K7KWA7 View 3D Structure Click here
K7UU99 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
Q0E2A9 View 3D Structure Click here
Q4D8I3 View 3D Structure Click here
Q4D8I4 View 3D Structure Click here
Q4DEY9 View 3D Structure Click here
Q4DJU9 View 3D Structure Click here
Q4DUG0 View 3D Structure Click here
Q54H31 View 3D Structure Click here
Q54JI4 View 3D Structure Click here
Q54KJ2 View 3D Structure Click here
Q54T92 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

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;