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3  structures 1400  species 0  interactions 7648  sequences 149  architectures

Family: CLTH (PF10607)

Summary: CTLH/CRA C-terminal to LisH motif domain

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CTLH/CRA C-terminal to LisH motif domain Provide feedback

RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [5]. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif [6].

Literature references

  1. Nakamura M, Masuda H, Horii J, Kuma K, Yokoyama N, Ohba T, Nishitani H, Miyata T, Tanaka M, Nishimoto T; , J Cell Biol. 1998;143:1041-1052.: When overexpressed, a novel centrosomal protein, RanBPM, causes ectopic microtubule nucleation similar to gamma-tubulin. PUBMED:9817760 EPMC:9817760

  2. Wu Y, Sun X, Kaczmarek E, Dwyer KM, Bianchi E, Usheva A, Robson SC; , Biochem J. 2006;396:23-30.: RanBPM associates with CD39 and modulates ecto-nucleotidase activity. PUBMED:16478441 EPMC:16478441

  3. Denti S, Sirri A, Cheli A, Rogge L, Innamorati G, Putignano S, Fabbri M, Pardi R, Bianchi E; , J Biol Chem. 2004;279:13027-13034.: RanBPM is a phosphoprotein that associates with the plasma membrane and interacts with the integrin LFA-1. PUBMED:14722085 EPMC:14722085

  4. Murrin LC, Talbot JN; , J Neuroimmune Pharmacol. 2007;2:290-295.: RanBPM, a scaffolding protein in the immune and nervous systems. PUBMED:18040864 EPMC:18040864

  5. Menon RP, Gibson TJ, Pastore A; , J Mol Biol. 2004;343:43-53.: The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre. PUBMED:15381419 EPMC:15381419

  6. Emes RD, Ponting CP;, Hum Mol Genet. 2001;10:2813-2820.: A new sequence motif linking lissencephaly, Treacher Collins and oral-facial-digital type 1 syndromes, microtubule dynamics and cell migration. PUBMED:11734546 EPMC:11734546


This tab holds annotation information from the InterPro database.

InterPro entry IPR024964

RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. The RanBPM protein contains multiple conserved domains that provide potential protein-protein interaction sites [ PUBMED:22094242 ]. This entry represents a domain at the C terminus of RanBPM containing the CT11-RanBPM (CRA) motif. The CRA motif was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [ PUBMED:15381419 ]. The region comprising this domain contains the CTLH and CRA domains annotated by SMART; however, these may be a single domain, and is referred to as a C-terminal to LisH motif [ PUBMED:11734546 ].

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
(115)
Full
(7648)
Representative proteomes UniProt
(12620)
RP15
(1399)
RP35
(3575)
RP55
(6068)
RP75
(8182)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(115)
Full
(7648)
Representative proteomes UniProt
(12620)
RP15
(1399)
RP35
(3575)
RP55
(6068)
RP75
(8182)
Alignment:
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Sequence:
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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
(115)
Full
(7648)
Representative proteomes UniProt
(12620)
RP15
(1399)
RP35
(3575)
RP55
(6068)
RP75
(8182)
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_3765 (release 22.0), UPF0559
Previous IDs: RanBPM_CRA;
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P , Bateman A
Number in seed: 115
Number in full: 7648
Average length of the domain: 171.40 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 39.38 %

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 26.0 26.0
Trusted cut-off 26.0 26.1
Noise cut-off 25.9 25.9
Model length: 150
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 CLTH domain has been found. There are 3 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
A0A1D6GAF1 View 3D Structure Click here
A0A1D6HAK4 View 3D Structure Click here
A0A1D6JVD0 View 3D Structure Click here
A0A1D6LYW8 View 3D Structure Click here
A0A1D6Q353 View 3D Structure Click here
A0A1D8PM68 View 3D Structure Click here
A0A1P8B5A1 View 3D Structure Click here
A0A368UHM1 View 3D Structure Click here
A1L252 View 3D Structure Click here
B4FSH1 View 3D Structure Click here
C0PFM0 View 3D Structure Click here
C4IZE2 View 3D Structure Click here
C6T9V4 View 3D Structure Click here
D3Z7Z5 View 3D Structure Click here
D3ZWU9 View 3D Structure Click here
E7FGY2 View 3D Structure Click here
F1LVV3 View 3D Structure Click here
F4HYD7 View 3D Structure Click here
F4I7D4 View 3D Structure Click here
F4K250 View 3D Structure Click here
I1J6W1 View 3D Structure Click here
I1K211 View 3D Structure Click here
I1K7N3 View 3D Structure Click here
I1KW85 View 3D Structure Click here
I1KX38 View 3D Structure Click here
I1LNN1 View 3D Structure Click here
I1M296 View 3D Structure Click here
I1M2J4 View 3D Structure Click here
I1M875 View 3D Structure Click here
I1ME36 View 3D Structure Click here
I1MED3 View 3D Structure Click here
K7MM68 View 3D Structure Click here
K7MM68 View 3D Structure Click here
K7MNY1 View 3D Structure Click here
K7N5D9 View 3D Structure Click here
O18188 View 3D Structure Click here
O59668 View 3D Structure Click here
O94712 View 3D Structure Click here
P40208 View 3D Structure Click here
P40492 View 3D Structure Click here
P53076 View 3D Structure Click here
P69566 View 3D Structure Click here
Q10446 View 3D Structure Click here
Q10PG5 View 3D Structure Click here
Q12508 View 3D Structure Click here
Q1LUS8 View 3D Structure Click here
Q338W3 View 3D Structure Click here
Q4VC33 View 3D Structure Click here
Q4Z8K6 View 3D Structure Click here
Q54CT2 View 3D Structure Click here
Q54PM0 View 3D Structure Click here
Q54X16 View 3D Structure Click here
Q555R9 View 3D Structure Click here
Q566Q9 View 3D Structure Click here
Q59RB2 View 3D Structure Click here
Q5A4G9 View 3D Structure Click here
Q5RKJ1 View 3D Structure Click here
Q5ZAY8 View 3D Structure Click here
Q69K99 View 3D Structure Click here
Q6ATC3 View 3D Structure Click here
Q6PBS0 View 3D Structure Click here
Q6PC55 View 3D Structure Click here
Q6VN19 View 3D Structure Click here
Q6VN20 View 3D Structure Click here
Q6YDN8 View 3D Structure Click here
Q6ZI83 View 3D Structure Click here
Q7L5Y9 View 3D Structure Click here
Q7SXR3 View 3D Structure Click here
Q80YQ8 View 3D Structure Click here
Q84WK5 View 3D Structure Click here
Q8IDW7 View 3D Structure Click here
Q8IE21 View 3D Structure Click here
Q8MSB1 View 3D Structure Click here
Q8RX25 View 3D Structure Click here
Q8SZN4 View 3D Structure Click here
Q91YQ7 View 3D Structure Click here
Q94BS7 View 3D Structure Click here
Q96G75 View 3D Structure Click here
Q96S59 View 3D Structure Click here
Q9D7M1 View 3D Structure Click here
Q9H871 View 3D Structure Click here
Q9LXC7 View 3D Structure Click here
Q9M2V9 View 3D Structure Click here
Q9NWU2 View 3D Structure Click here
Q9T075 View 3D Structure Click here
Q9UAU3 View 3D Structure Click here
Q9URU9 View 3D Structure Click here
Q9VWS1 View 3D Structure Click here
Q9W2N5 View 3D Structure Click here
Q9ZQ45 View 3D Structure Click here