Summary: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
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RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) Provide feedback
The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.
Birney E., Kumar S., Krainer A.R. , Nucleic Acid Res 1993;21:5803-5816.: Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. PUBMED:8290338 EPMC:8290338
Internal database links
|SCOOP:||Smg4_UPF3 RRM_2 Calcipressin Nup35_RRM NID BRAP2 RNA_bind RRM_3 DUF1866 Nab6_mRNP_bdg Limkain-b1 SET_assoc RRM_5 RRM_6 Nup35_RRM_2 DUF4523 Spo7_2_N DUF4651 RRM_7 RRM_occluded|
|Similarity to PfamA using HHSearch:||Smg4_UPF3 RRM_2 Calcipressin Nup35_RRM BRAP2 RNA_bind RRM_3 Limkain-b1 SET_assoc RRM_5 RRM_6 Nup35_RRM_2 RRM_7 RRM_occluded|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000504
Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [PUBMED:3072706, PUBMED:3192525, PUBMED:3313012]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [PUBMED:2470643, PUBMED:2467746]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [PUBMED:3192525, PUBMED:3313012, PUBMED:2467746]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition [PUBMED:15231733]. The motif also appears in a few single stranded DNA binding proteins.
The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases [PUBMED:8290338]. The RRM is reviewed in a number of publications [PUBMED:1716386, PUBMED:15853797, PUBMED:16387655].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||nucleic acid binding (GO:0003676)|
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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 17 members:BRAP2 Calcipressin DUF1866 Limkain-b1 Nup35_RRM Nup35_RRM_2 RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_6 RRM_7 RRM_occluded Smg4_UPF3 Tap-RNA_bind XS
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Author:||Eddy SR, Birney E|
|Number in seed:||72|
|Number in full:||97323|
|Average length of the domain:||67.70 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||23.75 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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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_1 domain has been found. There are 594 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 seqence.
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