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72  structures 393  species 0  interactions 8811  sequences 359  architectures

Family: RRM_6 (PF14259)

Summary: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain)

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This is the Wikipedia entry entitled "RNA recognition motif". More...

RNA recognition motif Edit Wikipedia article

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Identifiers
Symbol RRM_1
Pfam PF00076
Pfam clan RRM CL0221 RRM
InterPro IPR000504
PROSITE PDOC00030
SCOP 1sxl
SUPERFAMILY 1sxl

RNA recognition motif, RNP-1 is a putative RNA-binding domain of about 90 amino acids that are known to bind single-stranded RNAs. It was found in many eukaryotic proteins.[1][2][3]

The largest group of single strand RNA-binding protein is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence.[4][5]

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).[2][3][5] The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor appears to have two RRM-like domains with specialised features for protein recognition.[6] 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.[7] The RRM is reviewed in a number of publications.[8][9][10]

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;

References

  1. ^ 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. 
  2. ^ a b 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. 
  3. ^ a b 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. 
  4. ^ 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. 
  5. ^ a b 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. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ 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. 
  10. ^ 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. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR000504

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

RNA recognition motif (a.k.a. RRM, RBD, or RNP domain) Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

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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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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 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

Alignments

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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
(76)
Full
(8811)
Representative proteomes NCBI
(52886)
Meta
(951)
RP15
(1680)
RP35
(2599)
RP55
(3942)
RP75
(5363)
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Format an alignment

  Seed
(76)
Full
(8811)
Representative proteomes NCBI
(52886)
Meta
(951)
RP15
(1680)
RP35
(2599)
RP55
(3942)
RP75
(5363)
Alignment:
Format:
Order:
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
(76)
Full
(8811)
Representative proteomes NCBI
(52886)
Meta
(951)
RP15
(1680)
RP35
(2599)
RP55
(3942)
RP75
(5363)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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.

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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: JCSG:Target_421663_WS20613B
Previous IDs: none
Type: Domain
Author: Coggill P
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 18.0
Trusted cut-off 27.0 18.0
Noise cut-off 26.9 17.9
Model length: 70
Family (HMM) version: 1
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 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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