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4  structures 759  species 0  interactions 1566  sequences 42  architectures

Family: RRM_3 (PF08777)

Summary: RNA binding motif

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RNA binding motif Provide feedback

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif [1].

Literature references

  1. Jacks A, Babon J, Kelly G, Manolaridis I, Cary PD, Curry S, Conte MR; , Structure. 2003;11:833-843.: Structure of the C-terminal domain of human La protein reveals a novel RNA recognition motif coupled to a helical nuclear retention element. PUBMED:12842046 EPMC:12842046

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014886

This entry represents the atypical RRM, named xRRM, found in La and La-related proteins (LaRPs). They belong to an ancient superfamily of proteins that are conserved in nearly all eukaryotes, except Plasmodium. These proteins are broadly involved in critical processes of RNA use and metabolism in the nucleus and the cytoplasm. The LaRP superfamily is distinguished by a conserved bipartite RNA-binding unit called the La-module, composed by a Lupus antigen motif (LaM) followed by an RNA-Recognition motif (RRM). Beyond this, each LaRP family is characterized by distinct family specific domains and motifs that contribute to structure and function. Genuine La and La-related proteins group 7 (LARP7) bind to the non-coding RNAs transcribed by RNA polymerase III (RNAPIII), which end in UUU. The La-module of these proteins bind the UUU-3'OH, protecting the RNA from degradation, while other domains may be important for RNA folding or others functions. The La and LaRP7 protein families have a C-terminal domain that contains a novel class of atypical RRM, named xRRM (for atypical RRM with extended alpha3), which uses a unique mode of single- and double-strand RNA binding [ PUBMED:12842046 , PUBMED:22705372 , PUBMED:23328630 , PUBMED:27679474 , PUBMED:31752575 ].

The overall fold of the xRRM is an RRM, but with several atypical features. Unusual features of the xRRM include the absence of conserved RNP1 and RNP2 aromatic sequences on the beta3 and beta1 strands, respectively, typically involved in nucleotide recognition; the presence of an additional helix alpha3 that lies across the beta-sheet surface, where single-stranded nucleotides usually bind; and a C-terminal tail required for RNA binding that is disordered in the free xRRM but forms an alpha3 extension (alpha3x) on binding RNA. The front face of the xRRM consists of an antiparallel beta-sheet with helix alpha3 lying across the beta-sheet perpendicular to the beta-strand axis. The back side of the xRRM consists of alpha helices. The xRRM interacts with both single- and double-stranded RNA using the beta-sheet surface and the C-terminal tail, which forms a helical extension of alpha3 (alhpa3x) that binds to the RNA major groove[ PUBMED:12842046 , PUBMED:22705372 , PUBMED:23328630 , PUBMED:27679474 , PUBMED:31752575 ].

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 RRM (CL0221), which has the following description:

This clan contains families that are related to the RNA recognition motif domains. However, not all these families are RNA binding.

The clan contains the following 33 members:

BRAP2 Calcipressin DbpA DUF1743 DUF1866 DUF4523 GlcNAc-1_reg GUCT MARF1_RRM1 Nup35_RRM Nup35_RRM_2 PHM7_cyt Ret2_MD RL RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_8 RRM_9 RRM_occluded RRM_Rrp7 SET_assoc Smg4_UPF3 Spo7_2_N Tap-RNA_bind Transposase_22 U1snRNP70_N xRRM XS YlmH_RBD


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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: pdb_1owx
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J
Number in seed: 11
Number in full: 1566
Average length of the domain: 100.5 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 21.14 %

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 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 102
Family (HMM) version: 14
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


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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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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 RRM_3 domain has been found. There are 4 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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