TABLE 1.
Overview of the Most Frequently Encountered RBDs and Examples of RBPs Comprising These Domains
| Domain | Domain Description | Gene Symbol | Gene Alias | Reference |
|---|---|---|---|---|
| RRM | RRMs are found in a variety of RBPs, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. | CELF1 | CUGBP1 | 5 |
| zf-C2H2_jaz | Mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ—dsRNA-binding ZF protein—zinc fingers. | ZNF346 | JAZ,Zfp346 | 6 |
| zf-CCCH | Zinc finger C-x8-C-x5-C-x3-H type (and similar). Found in many known RBPs. | ZFP36 | TTP;TIS11; NUP475; RNF162A | 7,8 |
| KH | K homology RBD, type I. KH binds single-stranded RNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. | HNRNPK | CSBP; TUNP; HNRPK | 9 |
| G-patch | Found in a number of RBPs, and is also found in proteins that contain RBDs. This domain has seven highly conserved glycines. | RBM5 | LUCA15,LUCA | 10 |
| LSM | The like SM (LSM) domain contains Sm proteins as well as other related LSM (like Sm) proteins. | LSM1–7 | 11 | |
| SAP | The SAP (after SAF-A/B, Acinus, and PIAS) motif is a putative DNA/RBD found in diverse nuclear and cytoplasmic proteins. | HNRNPU | 12 | |
| zf-RanBP | Zn-finger found in Ran-binding protein and others. | TAF15 | Npl3, RBP56, TAF2N, TAFII68, hTAFII68 | 13 |
| zf-CCHC | The zinc knuckle is a zinc-binding motif composed of the following CX2CX4HX4C where X can be any amino acid. | ZCCHC11 | PAPD3, TUT4 | 14 |
| HABP4_PAI-RBP1 | This family includes the hyaluronan-binding protein 4 (HABP4) family of hyaluronan-binding proteins, and the PAI-1 mRBP, PAI-RBP1. | SERBP1 | CGI-55, CHD3IP, HABP4L, PAI-RBP1, PAIRBP1 | 15 |
| dsrm | Double-stranded RNA-binding motif. Found in a variety of proteins including dsRNA-dependent protein kinase protein kinase R (PKR), RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA-dependent adenosine deaminases. | STAU1 | STAU | 16 |
| TUDOR | Often thought to act as protein–protein interaction domain and some protein members of this domain class recognize dimethylated arginines. For some family members RNA binding has also been observed. | SMN1 | SMN, SMN2, SMNT | 17 |
| MIF4G | MIF4G is named after middle domain of eukaryotic initiation factor 4G (eIF4G). The domain is rich in α helices and may contain multiple α-helical repeats. | EIF4G | EIF-4G1, EIF4F, EIF4G, EIF4GI, P220 | 18 |
| PAZ | This domain is named PAZ after the proteins Piwi Argonaut and Zwille. PAZ can bind the characteristic two-base 3′ overhangs of siRNAs. | EIF2C1–4 | AGO1–4, Argonaute 1–4 | 19,20 |
| RBM1CTR | This C-terminal region is found in RBM1-like RNA-binding hnRNPs. | RBMX | HNRPG,RBMXP1 RBMXRT, RNMX hnRNP-G | 21 |
| S1 | The S1 domain occurs in a wide range of RNA-associated proteins. | DHX8 | DDX8, HRH1, PRP22 PRPF22 | 22 |
| Piwi | This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. | EIF2C1–4 | AGO1–4, Argonaute 1–4 | 19,20 |
| cold shock domain (CSD) | RBD that functions as a RNA chaperone in bacteria and is involved in regulating translation in eukaryotes. | LIN28B | CSDD2 | 23 |
RBDs, RNA-binding domains; RBPs, RNA-binding proteins; RNPs, ribonucleoprotein complexes.