spacer
spacer
EBIDatabasesInterPro

Jump to: InterProScan Databases Documentation FTP site Help
Click on the icon for context sensitive help from the user manual.
Advanced search

InterPro: IPR000504 RNA recognition motif, RNP-1

Protein matchesHelp
Open in usermanual
UniProtKB
Matches:
18711 proteins
AccessionHelp
Open in usermanual
IPR000504 RRM_RNP1
TypeHelp
Open in usermanual
Domain
SignaturesHelp
Open in usermanual
InterPro RelationshipsHelp
Open in usermanual
Children IPR003954 RNA recognition, domain 1
Found in IPR002343 Paraneoplastic encephalomyelitis antigen
IPR002344 Lupus La protein
IPR006509 Splicing factor, CC1-like
IPR006515 Polyadenylate binding protein, human types 1, 2, 3, 4
IPR006529 U2 snRNP auxilliary factor, large subunit, splicing factor
IPR006532 Poly-U binding splicing factor, half-pint
IPR006535 HnRNP R/Q splicing factor
IPR006536 HnRNP-L/PTB/hephaestus splicing factor
IPR006546 Sex-lethal splicing factor
IPR006548 Splicing factor ELAV/HuD
IPR008111 RNA binding motif protein 8
IPR009145 U2 auxiliary factor small subunit
IPR011400 Translation initiation factor eIF-3b
IPR012677 Nucleotide-binding, alpha-beta plait
IPR015462 Y chromosome RNA recognition motif
IPR015463 RNA recognition motif, SEB4-related
IPR015464 RNA recognition motif-related
IPR015465 RNA recognition motif, glycine rich protein
IPR015466 RNA binding motif 4 - LARK
IPR016304 Peptidyl-prolyl cis-trans isomerase E
IPR016967 Splicing factor, SPF45
IPR017111 Histone H3-K4 methyltransferase Set1, fungal
IPR017325 RNA-binding protein 9/Ataxin-2-binding protein
IPR017334 Translation initiation factor 3, RNA-binding subunit
IPR017347 Heterogeneous nuclear ribonucleoprotein C, Raly
GO Term annotationHelp
Open in usermanual
Function GO:0003676 nucleic acid binding
InterPro annotation
BioMart Logo Entry Details in BioMart
AbstractHelp
Open in usermanual

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 [1, 2, 3]. 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 [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, U2AF, 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 (U2AF) 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. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases [7]. The RRM is reviewed in a number of publications [8, 9, 10].
Structural linksHelp
Open in usermanual
PDB - click here
1a9n , 1aud , 1b7f , 1cvj , 1cx0 , 1d8z , 1d9a , 1drz , 1dz5 , 1fht , 1fj7 , 1fjc , 1fje , 1fnx , 1fxl , 1g2e , 1h2t , 1h2u , 1h2v , 1h6k , 1ha1 , 1hd0 , 1hd1 , 1hl6 , 1iqt , 1jmt , 1l3k , 1m5k , 1m5o , 1m5p , 1m5v , 1n52 , 1n54 , 1no8 , 1nu4 , 1o0p , 1oia , 1oo0 , 1opi , 1owx , 1p1t , 1p27 , 1pgz , 1po6 , 1qm9 , 1rk8 , 1rkj , 1s79 , 1sj3 , 1sj4 , 1sjf , 1sjq , 1sjr , 1sxl , 1u1k , 1u1l , 1u1m , 1u1n , 1u1o , 1u1p , 1u1q , 1u1r , 1u2f , 1u6b , 1u6f , 1uaw , 1ufw , 1up1 , 1urn , 1vbx , 1vby , 1vbz , 1vc0 , 1vc5 , 1vc6 , 1vc7 , 1wel , 1wex , 1wez , 1wf0 , 1wf1 , 1wf2 , 1wg1 , 1wg4 , 1wg5 , 1whw , 1whx , 1why , 1wi6 , 1wi8 , 1wtb , 1x0f , 1x4a , 1x4b , 1x4c , 1x4d , 1x4e , 1x4f , 1x4g , 1x4h , 1x5o , 1x5p , 1x5s , 1x5t , 1x5u , 1yty , 1zh5 , 1zzn , 2ad9 , 2adb , 2adc , 2aym , 2b0g , 2bz2 , 2cpd , 2cpe , 2cpf , 2cph , 2cpi , 2cpj , 2cpx , 2cpy , 2cpz , 2cq0 , 2cq1 , 2cq3 , 2cq4 , 2cqb , 2cqc , 2cqd , 2cqg , 2cqh , 2cqi , 2cqp , 2dgs , 2dgx , 2dhg , 2dis , 2dit , 2dny , 2do0 , 2err , 2evz , 2f9d , 2f9j , 2ghp , 2hyi , 2hzc , 2j0q , 2j0s , 2jx2 , 2k3k , 2mss , 2mst , 2nz4 , 2o3d , 2oih , 2oj3 , 2pe8 , 2peh , 2sxl , 2u1a , 2u2f , 2up1 , 2vod , 2von , 2voo , 2vop , 3beg , 3bo2 , 3bo3 , 3bo4 , 3cul , 3cun , 3sxl
SCOP: d.58.7.1 , d.58.7.3
CATH: 3.30.70.330
Database linksHelp
Open in usermanual
PROSITE doc: PDOC00030
PANDIT: PF00076
Blocks: IPB000504
Pfam Clan: CL0221.7

Taxonomic coverageHelp
Open in usermanual

Overlapping InterPro entriesHelp
Open in usermanual
IPR000504 Numbers of overlapping proteins Average numbers of overlapping amino acids

Example proteinsHelp
Open in usermanual
A0AV96 RNA-binding protein 47

O01159 Probable splicing factor, arginine/serine-rich 7

O08583 THO complex subunit 4

P04147 Polyadenylate-binding protein, cytoplasmic and nuclear

P19339 Protein sex-lethal

More proteins


Example Proteins Key


InterPro entry accession number/name and structure databases Colour code
IPR006515 Polyadenylate binding protein, human types 1, 2, 3, 4
IPR012677 Nucleotide-binding, alpha-beta plait
IPR006546 Sex-lethal splicing factor
IPR002343 Paraneoplastic encephalomyelitis antigen
IPR000504 RNA recognition motif, RNP-1
IPR002004 Polyadenylate-binding protein/Hyperplastic disc protein
IPR006535 HnRNP R/Q splicing factor
SWISS-MODEL
PDB Chain
ModBase
CATH Domain
SCOP Domain

PublicationsHelp
Open in usermanual
1. Dreyfuss G, Swanson MS, Pinol-Roma S.
Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation.
Trends Biochem. Sci. 13 86-91 1988 [PubMed: 3072706]
http://dx.doi.org/10.1016/0968-0004(88)90046-1
2. Chambers JC, Kenan D, Martin BJ, Keene JD.
Genomic structure and amino acid sequence domains of the human La autoantigen.
J. Biol. Chem. 263 18043-51 1988 [PubMed: 3192525]
http://intl.jbc.org/cgi/reprint/263/34/18043.pdf
3. Sachs AB, Davis RW, Kornberg RD.
A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability.
Mol. Cell. Biol. 7 3268-76 1987 [PubMed: 3313012]
http://ukpmc.ac.uk/articlerender.cgi?tool=EBI&pubmedid=3313012
4. Bandziulis RJ, Swanson MS, Dreyfuss G.
RNA-binding proteins as developmental regulators.
Genes Dev. 3 431-7 1989 [PubMed: 2470643]
http://www.genesdev.org/cgi/content/abstract/3/4/431
5. Query CC, Bentley RC, Keene JD.
A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein.
Cell 57 89-101 1989 [PubMed: 2467746]
http://dx.doi.org/10.1016/0092-8674(89)90175-X
6. Kielkopf CL, Lucke S, Green MR.
U2AF homology motifs: protein recognition in the RRM world.
Genes Dev. 18 1513-26 2004 [PubMed: 15231733]
http://dx.doi.org/10.1101/gad.1206204
7. Birney E, Kumar S, Krainer AR.
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors.
Nucleic Acids Res. 21 5803-16 1993 [PubMed: 8290338]
http://dx.doi.org/10.1093/nar/21.25.5803
8. Kenan DJ, Query CC, Keene JD.
RNA recognition: towards identifying determinants of specificity.
Trends Biochem. Sci. 16 214-20 1991 [PubMed: 1716386]
http://dx.doi.org/10.1016/0968-0004(91)90088-D
9. Maris C, Dominguez C, Allain FH.
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
FEBS J. 272 2118-31 2005 [PubMed: 15853797]
http://dx.doi.org/10.1111/j.1742-4658.2005.04653.x
10. Teplova M, Yuan YR, Phan AT, Malinina L, Ilin S, Teplov A, Patel DJ.
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 75-85 2006 [PubMed: 16387655]
http://dx.doi.org/10.1016/j.molcel.2005.10.027

Additional ReadingHelp
Open in usermanual
Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S.
Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein.
Structure 16 2008 852-62 [PubMed: 18547518]
http://dx.doi.org/10.1016/j.str.2008.02.021
Rebagliati M.
An RNA recognition motif in the bicoid protein.
Cell 58 1989 231-2 [PubMed: 2752425]
http://dx.doi.org/10.1016/0092-8674(89)90834-9
Ayane M, Preuss U, Kohler G, Nielsen PJ.
A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs.
Nucleic Acids Res. 19 1991 1273-8 [PubMed: 2030943]
http://dx.doi.org/10.1093/nar/19.6.1273
Ngo JC, Giang K, Chakrabarti S, Ma CT, Huynh N, Hagopian JC, Dorrestein PC, Fu XD, Adams JA, Ghosh G.
A sliding docking interaction is essential for sequential and processive phosphorylation of an SR protein by SRPK1.
Mol. Cell 29 2008 563-76 [PubMed: 18342604]
http://dx.doi.org/10.1016/j.molcel.2007.12.017
Kawakami A, Tian Q, Duan X, Streuli M, Schlossman SF, Anderson P.
Identification and functional characterization of a TIA-1-related nucleolysin.
Proc. Natl. Acad. Sci. U.S.A. 89 1992 8681-5 [PubMed: 1326761]
http://ukpmc.ac.uk/articlerender.cgi?tool=EBI&pubmedid=1326761
Szabo A, Dalmau J, Manley G, Rosenfeld M, Wong E, Henson J, Posner JB, Furneaux HM.
HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and Sex-lethal.
Cell 67 1991 325-33 [PubMed: 1655278]
http://dx.doi.org/10.1016/0092-8674(91)90184-Z
Lipchock SV, Strobel SA.
A relaxed active site after exon ligation by the group I intron.
Proc. Natl. Acad. Sci. U.S.A. 105 2008 5699-704 [PubMed: 18408159]
http://dx.doi.org/10.1073/pnas.0712016105
Milburn SC, Hershey JW, Davies MV, Kelleher K, Kaufman RJ.
Cloning and expression of eukaryotic initiation factor 4B cDNA: sequence determination identifies a common RNA recognition motif.
EMBO J. 9 1990 2783-90 [PubMed: 2390971]
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=2390971
Li YQ, Sugiura M.
Three distinct ribonucleoproteins from tobacco chloroplasts: each contains a unique amino terminal acidic domain and two ribonucleoprotein consensus motifs.
EMBO J. 9 1990 3059-66 [PubMed: 1698606]
http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=EBI&pubmedid=1698606&action=stream&blobtype=pdf
Rao JN, Schweimer K, Wenzel S, Wohrl BM, Rosch P.
NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding.
Biochemistry 47 2008 3756-61 [PubMed: 18303858]
http://dx.doi.org/10.1021/bi702429m
Xiao H, Murakami H, Suga H, Ferre-D'Amare AR.
Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.
Nature 454 2008 358-61 [PubMed: 18548004]
http://dx.doi.org/10.1038/nature07033
spacer
spacer
Page rendered:
Database: IWEB
Request
Host tomcat-7.ebi.ac.uk
Server up Wed Nov 25 16:52:18 GMT 2009
Initialise JS Log Login settings Flush
InterPro 23.1