Table 1. List of known and putative dsRBD folds in human proteins, and databases that identify them.
| Identified in InterPro database as a dsRBDd |
|||||||
|---|---|---|---|---|---|---|---|
| Protein / UniProtKB accession numbera |
Amino acid number in representative isoformb |
dsRBD nomenclature |
Amino acids in dsRBD (dsRBD size)c |
Gene3D (CATH) |
SMART | Prosite | Pfam |
| A1CF / Q9NQ94 | 594 | 1 | 446-523 (78) | Y | N | N | N |
| ADAD1 / Q96M93 | 576 | 1 | 96-164 (69) | Y | Y | Y | Y |
| ADAD2 / Q8NCV1 | 583 | 1 | 115-181 (67) | Y | Y | Y | Y |
| ADAR1 / P55265 | 1226 | 1 | 502-571 (70) | Y | Y | Y | Y |
| 2 | 614-682 (69) | Y | Y | Y | Y | ||
| 3 | 725-794 (70) | Y | Y | Y | Y | ||
| ADAR2 / P78563 | 741 | 1 | 78-146 (69) | Y | Y | Y | Y |
| 2 | 232-299 (68) | Y | Y | Y | Y | ||
| ADAR3 / Q9NS39 | 739 | 1 | 125-193 (69) | Y | Y | Y | Y |
| 2 | 274-342 (69) | Y | Y | Y | Y | ||
| CDKN2AIP / Q9NXV6 | 580 | 1 | 462-537 (76) | Y | N | Y | N |
| DGCR8 / Q8WYQ5 | 773 | 1 | 501-586 (67) | Y | Y | Y | Y |
| 2 | 620-685 (66) | N | Y | N | Y | ||
| DHX9 / Q08211 | 1270 | 1 | 3-73 (71) | Y | Y | Y | Y |
| 2 | 180-254 (75) | Y | Y | Y | Y | ||
| DHX30 / Q7L2E3 | 1222 | 1 | 80-153 (74) | N | N | N | N |
| 2 | 273-342 (70) | N | N | N | N | ||
| Dicer / Q9UPY3 | 1922 | 1 (DUF283) | 630-722 (80) | N | N | N | N |
| C-terminal | 1849-1918 (70) | Y | N | Y | N | ||
| Drosha / Q9NRR4 | 1374 | 1 | 1259-1334 (76) | Y | Y | Y | Y |
| DUS2/ Q9NX74 | 493 | 1 | 369-435 (67) | Y | Y | N | Y |
| ILF3 / Q12906 | 894 | 1 | 398-467 (70) | Y | Y | Y | Y |
| 2 | 524-590 (67) | Y | Y | Y | Y | ||
| Kanadaptin / Q9BWU0 | 796 | 1 | 370-439 (70) | N | Y | N | Y |
| NkRF / O15226 | 690 | 1 | 349-411 (63) | Y | Y | N | N |
| 2 | 451-512 (62) | N | Y | N | N | ||
| PACT / O75569 | 313 | 1 | 34-101 (68) | Y | Y | Y | Y |
| 2 | 126-194 (69) | Y | Y | Y | Y | ||
| 3 | 239-308 (70) | Y | Y | Y | N | ||
| PKR / P19525 | 551 | 1 | 8-81 (74) | Y | Y | Y | Y |
| 2 | 99-171 (73) | Y | Y | Y | Y | ||
| SON / P18583 | 2140 | 1 | 2053-2120 (68) | Y | Y | Y | Y |
| 2426 | 1 ΔC-terminus | 2371-2412 (42) | Y | N | Y | N | |
| STAU1 / Q6PJX3 | 577 | 2 | 69-164 (96) | Y | Y | Y | Y |
| 3 | 180-260 (67) | Y | Y | Y | Y | ||
| 4 | 283-365 (67) | Y | Y | Y | Y | ||
| 5 | 488-554 (67) | N | N | N | N | ||
| STAU2 / Q9NUL3 | 570 | 1 | 3-87 (85) | Y | Y | Y | Y |
| 2 | 91-184 (94) | Y | Y | Y | Y | ||
| 3 | 203-284 (67) | Y | Y | Y | Y | ||
| 4 | 303-381 (67) | Y | Y | Y | Y | ||
| 5 Δmiddle | 496-521 (26) | N | N | N | N | ||
| STRBP / Q96SI9 | 672 | 1 | 387-453 (67) | Y | Y | Y | Y |
| 2 | 510-578 (69) | Y | Y | Y | Y | ||
| TARBP2 / Q15633 | 366 | 1 | 27-100 (74) | Y | Y | Y | Y |
| 2 | 159-227 (69) | Y | Y | Y | Y | ||
| 3 | 294-361 (68) | Y | Y | Y | N | ||
| Protein / UniProtKB accession numbere |
Ribosome typef |
Amino acid number in representative isoformb |
dsRBDg or dsRBD-like fold nomenclature |
Amino acids in dsRBD or dsRBD- like fold (dsRBD or dsRBD-like fold size)c |
Gene3D (CATH) |
SMART | Prosite | Pfam |
|---|---|---|---|---|---|---|---|---|
| C12orf65 / Q9H3J6 | mitochondrial | 166 | 1 | 53-125 (73) | Y | N | N | N |
| ICT1 / Q14197 | mitochondrial | 206 | 1 | 72-163 (92) | N | N | N | N |
| L44mt / Q9H9J2 | mitochondrial | 332 | 1 | 236-306 (71) | Y | N | Y | N |
| MRF-1 / O75570 | mitochondrial | 445 | 1g | 289-367 (79) | Y | N | N | N |
| RPS2/ P15880 | cytoplasmic | 293 | 1 | 98-167 (70) | Y | N | N | N |
| S5mt / P82675 | mitochondrial | 430 | 1 | 215-283 (69) | Y | N | N | N |
Full length protein names and identifiers (UniProtKB [http://www.uniprot.org/]) are as follows: A1CF, apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1) complementation factor; ADAD, adenosine deaminase domain-containing protein; ADAR, adenosine deaminase that acts on RNA; CDKN2AIP, cyclin-dependent kinase inhibitor 2A-interacting protein; DGCR8, DiGeorge syndrome critical region 8; DHX9, DEAH box protein 9, also called ATPdependent RNA helicase A; DHX30, DEAH box protein 30, also called putative ATP-dependent RNA helicase DHX30; Dicer, endoribonuclease; Drosha, RNase III; DUS2, dihydrouridine synthase 2, also called tRNA-dihydrouridine(20) synthase nicotinamide adenine dinucleotide phosphate-like; ILF3, interleukin enhancer-binding factor 3; NκRF, nuclear factor kappa-light-chain enhancer of activated B cells-repressing factor; PACT, protein activator of the interferon-induced, dsRNA-activated protein kinase (PKR); PKR, also called protein kinase RNA-activated; kanadaptin; human lung cancer oncogene 3 protein; SON, Bax antagonist selected in saccharomyces 1; STAU, Staufen dsRNAbinding protein; STRBP, spermatid perinuclear RNA-binding protein; TARBP2, trans-activationresponsive RNA-binding protein.
Representative isoform harbors the largest number of complete dsRBDs.
dsRBD boundaries are derived from InterPro or manually edited based on available structural information.
Note that InterPro (https://www.ebi.ac.uk/interpro/) and the four programs that it uses – Genomic Threading Database (Gene3d; http://gene3d.biochem.ucl.ac.uk/Gene3D/) based on Class, Architecture, Topology and Homology (CATH) protein assignments; the Simple Modular Architecture Research Tool (SMART; http://smart.embl-heidelberg.de/); Prosite (http://prosite.expasy.org/prosite.html); and the Protein families (Pfam; http://pfam.sanger.ac.uk/) – are constantly being updated. Thus, future results might differ from those we collected for this review. N, not found using default search parameters of InterPro; “Y”, found using default search parameters of InterPro.
Full length protein names and UniProtKB identifiers of dsRBD or dsRBD-like folds that majorly interact with ribosomes.
Type of ribosome that associates with this dsRBD or dsRBD-like fold. C12orf65, probable peptide chain release factor C12orf65, mitochondrial; ICT1, immature colon carcinoma transcript 1; L44mt, protein L44 of the mitochondrial 39S ribosomal subunit; MRF-1, mitochondrial peptide chain release factor 1; RPS2, protein S2 of the 40S ribosomal subunit; S5mt, protein S5 of the 28S mitochondrial ribosome small subunit.
Conforms more closely to a dsRBD fold than does dsRBD-like folds.