Summary: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain)
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RNA recognition motif Edit Wikipedia article
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|RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)|
|Pfam clan||RRM CL0221 RRM|
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, U2AF2, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu). The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor appears to have two RRM-like domains with specialised features for protein recognition. 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. A third helix is present during RNA binding in some cases. The RRM is reviewed in a number of publications.
Human proteins containing this domain
A2BP1; ACF; BOLL; BRUNOL4; BRUNOL5; BRUNOL6; CCBL2; CGI-96; CIRBP; CNOT4; CPEB2; CPEB3; CPEB4; CPSF7; CSTF2; CSTF2T; CUGBP1; CUGBP2; D10S102; DAZ1; DAZ2; DAZ3; DAZ4; DAZAP1; DAZL; DNAJC17; DND1; EIF3S4; EIF3S9; EIF4B; EIF4H; ELAVL1; ELAVL2; ELAVL3; ELAVL4; ENOX1; ENOX2; EWSR1; FUS; FUSIP1; G3BP; G3BP1; G3BP2; GRSF1; HNRNPL; HNRPA0; HNRPA1; HNRPA2B1; HNRPA3; HNRPAB; HNRPC; HNRPCL1; HNRPD; HNRPDL; HNRPF; HNRPH1; HNRPH2; HNRPH3; HNRPL; HNRPLL; HNRPM; HNRPR; HRNBP1; HSU53209; HTATSF1; IGF2BP1; IGF2BP2; IGF2BP3; LARP7; MKI67IP; MSI1; MSI2; MSSP-2; MTHFSD; MYEF2; NCBP2; NCL; NOL8; NONO; P14; PABPC1; PABPC1L; PABPC3; PABPC4; PABPC5; PABPN1; POLDIP3; PPARGC1; PPARGC1A; PPARGC1B; PPIE; PPIL4; PPRC1; PSPC1; PTBP1; PTBP2; PUF60; RALY; RALYL; RAVER1; RAVER2; RBM10; RBM11; RBM12; RBM12B; RBM14; RBM15; RBM15B; RBM16; RBM17; RBM18; RBM19; RBM22; RBM23; RBM24; RBM25; RBM26; RBM27; RBM28; RBM3; RBM32B; RBM33; RBM34; RBM35A; RBM35B; RBM38; RBM39; RBM4; RBM41; RBM42; RBM44; RBM45; RBM46; RBM47; RBM4B; RBM5; RBM7; RBM8A; RBM9; RBMS1; RBMS2; RBMS3; RBMX; RBMX2; RBMXL2; RBMY1A1; RBMY1B; RBMY1E; RBMY1F; RBMY2FP; RBPMS; RBPMS2; RDBP; RNPC3; RNPC4; RNPS1; ROD1; SAFB; SAFB2; SART3; SETD1A; SF3B14; SF3B4; SFPQ; SFRS1; SFRS10; SFRS11; SFRS12; SFRS15; SFRS2; SFRS2B; SFRS3; SFRS4; SFRS5; SFRS6; SFRS7; SFRS9; SLIRP; SLTM; SNRP70; SNRPA; SNRPB2; SPEN; SR140; SRRP35; SSB; SYNCRIP; TAF15; TARDBP; THOC4; TIA1; TIAL1; TNRC4; TNRC6C; TRA2A; TRSPAP1; TUT1; U1SNRNPBP; U2AF1; U2AF2; UHMK1; ZCRB1; ZNF638; ZRSR1; ZRSR2; eIF4B;
- Swanson MS, Dreyfuss G, Pinol-Roma S (1988). "Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation". Trends Biochem. Sci. 13 (3): 86–91. doi:10.1016/0968-0004(88)90046-1. PMID 3072706.
- Keene JD, Chambers JC, Kenan D, Martin BJ (1988). "Genomic structure and amino acid sequence domains of the human La autoantigen". J. Biol. Chem. 263 (34): –. PMID 3192525.
- Davis RW, Sachs AB, Kornberg RD (1987). "A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability". Mol. Cell. Biol. 7 (9): –. PMC 367964. PMID 3313012.
- Bandziulis RJ, Swanson MS, Dreyfuss G (1989). "RNA-binding proteins as developmental regulators". Genes Dev. 3 (4): 431–437. doi:10.1101/gad.3.4.431. PMID 2470643.
- Keene JD, Query CC, Bentley RC (1989). "A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein". Cell 57 (1): –. doi:10.1016/0092-8674(89)90175-X. PMID 2467746.
- Green MR, Kielkopf CL, Lucke S (2004). "U2AF homology motifs: protein recognition in the RRM world". Genes Dev. 18 (13): 1513–1526. doi:10.1101/gad.1206204. PMC 2043112. PMID 15231733.
- Kumar S, Birney E, Krainer AR (1993). "Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors". Nucleic Acids Res. 21 (25): 5803–5816. doi:10.1093/nar/21.25.5803. PMC 310458. PMID 8290338.
- Keene JD, Kenan DJ, Query CC (1991). "RNA recognition: towards identifying determinants of specificity". Trends Biochem. Sci. 16 (6): –. doi:10.1016/0968-0004(91)90088-d. PMID 1716386.
- Allain FH, Dominguez C, Maris C (2005). "The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression". FEBS J 272 (9): –. doi:10.1111/j.1742-4658.2005.04653.x. PMID 15853797.
- Teplova M, Yuan YR, Patel DJ, Malinina L, Teplov A, Phan AT, Ilin S (2006). "Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen". Mol. Cell 21 (1): –. doi:10.1016/j.molcel.2005.10.027. PMID 16387655.
RNA recognition motif (a.k.a. RRM, RBD, or RNP domain) Provide feedback
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Internal database links
|Similarity to PfamA using HHSearch:||Nup35_RRM RRM_1 RNA_bind RRM_3 Limkain-b1 RRM_5 Nup35_RRM_2|
External database links
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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 15 members:BRAP2 Calcipressin DUF1866 Limkain-b1 Nup35_RRM Nup35_RRM_2 Ribosomal_L23 RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_6 Smg4_UPF3 XS
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Curation and family details
|Number in seed:||76|
|Number in full:||8811|
|Average length of the domain:||69.90 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||16.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|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_6 domain has been found. There are 72 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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