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9  structures 161  species 0  interactions 451  sequences 41  architectures

Family: FXMRP1_C_core (PF12235)

Summary: Fragile X-related 1 protein core C terminal

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Fragile X-related 1 protein core C terminal Provide feedback

This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with PF05641 PF00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions [3]. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs [2].

Literature references

  1. Huot ME, Bisson N, Davidovic L, Mazroui R, Labelle Y, Moss T, Khandjian EW;, Mol Biol Cell. 2005;16:4350-4361.: The RNA-binding protein fragile X-related 1 regulates somite formation in Xenopus laevis. PUBMED:16000371 EPMC:16000371

  2. Zalfa F, Achsel T, Bagni C;, Curr Opin Neurobiol. 2006;16:265-269.: mRNPs, polysomes or granules: FMRP in neuronal protein synthesis. PUBMED:16707258 EPMC:16707258

  3. Banerjee P, Schoenfeld BP, Bell AJ, Choi CH, Bradley MP, Hinchey P, Kollaros M, Park JH, McBride SM, Dockendorff TC;, J Neurosci. 2010;30:6782-6792.: Short- and long-term memory are modulated by multiple isoforms of the fragile X mental retardation protein. PUBMED:20463240 EPMC:20463240


This tab holds annotation information from the InterPro database.

InterPro entry IPR022034

This entry represents the core C-terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C terminus. The Glutamine-arginine rich region facilitates protein interactions [PUBMED:16000371, PUBMED:20463240]. Proteins containing this domain contain two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs [PUBMED:16707258].

Fragile X mental retardation 1 protein (FMR1P) , fragile X-related 1 protein (FXR1P) and fragile X-related 2 protein (FXR2P) are members of a small family of RNA-binding proteins that are thought to transport mRNA and to control their translation [PUBMED:16000371]. The proteins contain two KH domains and a RGG box that are characteristic motifs in RNA-binding proteins as well as nuclear localization and export signals.

Gene Ontology

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(27)
Full
(451)
Representative proteomes UniProt
(796)
NCBI
(2588)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(235)
RP75
(321)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(27)
Full
(451)
Representative proteomes UniProt
(796)
NCBI
(2588)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(235)
RP75
(321)
Alignment:
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Sequence:
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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
(27)
Full
(451)
Representative proteomes UniProt
(796)
NCBI
(2588)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(235)
RP75
(321)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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_2701 (release 23.0)
Previous IDs: FXR1P_C;
Type: Family
Author: Assefa S, Gavin OL
Number in seed: 27
Number in full: 451
Average length of the domain: 107.90 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 19.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.6 29.6
Trusted cut-off 29.7 29.7
Noise cut-off 28.6 28.9
Model length: 136
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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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 FXMRP1_C_core domain has been found. There are 9 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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