| E. coli a | Xtal b | LP (X) c | LP (C) d | TL (X) e | TL (C) d | d(CC) f | lpS g | D h | sp/bf i | TI j | Le | Cf | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| R1 | |||||||||||||
| 16S | 323:327 | 318:322 | U:A (rH) | U:A (99.6%) | GAG | GAG (97.6%) | 9.58 | 5' | A | 33332/bbmmm | X / S20 | H | IIA |
| 16S | 1315:1319 | 1296:1300 | U:A (rH) | U:A (99.7%) | GCA | GCA (87.9%) | 9.54 | 5' | A | 33332/bbmmm | X+Y / S14, S19 | H | IA |
| 16S | 1177:1181 | 1158:1162 | G:G (rH) | G:G (95.9%) | GAA | GAA (95.4%) | 12.42 | 5' | A | 33333/bbmmm | X+Y / S10 | M | IA |
| 23S | 306:310 | 313:317 | U:A (rH) | U:A (69.2%) | GGA | GGR (79.4%) | 9.67 | 5' | A | 33332/bbmmm | X+Y+Z / L24 | H | IA |
| 23S | 475:479 | 481:485 | U:A (rH) | U:A (82.0%) | GCA | GAA (85.4%) | 9.62 | 3' | A | 33332/bbmmm | X / L24 | M | IA |
| 23S | 499:503 | 505:509 | C:A (rH) | U:A (92.9%) | GAA | GAA (54.3%) | 9.76 | 5' | A | 33332/bbmmm | X / -- | M | IIA |
| 23S | 1282:1286 | 1388:1392 | U:A (rH) | U:A (83.8%), c:a (10.0%) | GAG | GAR (94.1%) | 9.78 | 5' | A | 33332/bbmmm | X / -- | H | IA |
| 23S | 328:332 | 335:339 | U:A (rH) | U:A (98.1%) | GAC | GAB (66.3%) | 9.50 | 5' | A | 32222/buuum | X+Y / L4, L24 | H | IB |
| R2 | |||||||||||||
| 23S | 567:571 | 624:628 | U:A (rH) | c:a (43.2%), u:u (31.7%) | UUG | UUG (96.4%) | 9.40 | 5' | A | 33332/bbmmm | Y / L15 | H | IA |
| tRNA | N/A | 54:58 | U:A (rH) | U:A (95.2%) | ΨCG | UCR (99.1%) | 9.77 | 5' | A | 33332/bbmmm | X+Y / -- | H | IA |
| R3 | |||||||||||||
| 16S | 956:960 | 933:937 | U:U (rWb) | U:U (99.6%) | UAA | UAA (97.7%) | 9.01 | 5' | A | 33332/bbmmm | Z-(G:C) / S19 | M | IB |
| 23S | 1082:1086 | 1186:1190 | C:G (rWC) | U:A (52.4%), c:g (46.8%) | UAA | UAA (83.4%) | 11.14 | 5' | A | 33333/bbmmm | Z-(G:C) / -- | M | IB |
| 23S | 1925:1929 | 1966:1970 | U:G (rWb) | C:G (54.9%), u:g (44.6%) | UAA | UAA (98.9%) | 11.90 | 5' | A | 32332/bmmmm | Z-(G:C) / -- | M | IB |
| 23S | 2562:2566 | 2597:2601 | U:A (rH) | U:A (68.8%), c:u (25.3%) | UAA | UAA (83.4%) | 9.53 | 5' | A | 33332/bbmmm | Z-(G:C) / L14 | M | IB |
| 23S | 319:323 | 326:330 | G:C (WC) | C:G (77.4%), g:c (16.3%) | AUA | RWA (68.0%) | 10.95 | 5' | P | 33222/MMumM | Z / L4 | M | IIB |
| 23S | 476:480 | 482:486 | G:A (S) | G:A (88.5%) | CAA | AAA (92.7%) | 9.39 | 5' | A | 33323/bmmmm | Z / L24 | M | IIB |
| 5S | 24:27 | 22:26 | G:C (NC) | g:m (45.2%), a:r (43.0%) | UUG | - (98.5%) | 9.22 | 5' | A | 32333/MMbbb | Z / -- | I | IB |
| R4 | |||||||||||||
| 23S | 1752:1756 | 1808:1812 | C:G (WC) | c:g (47.5%), g:c (35.7%) | GCA | GYA (65.3%) | 10.69 | 5' | A | 33333/bbmmb | Y+Z (G:C) / L24e | M | IB |
| 23S | 2447:2451 | 2482:2486 | G:A (H) | G:A (97.4%) | AUA | AUA (99.8%) | 12.83 | 5' | P | 22233/MmmMM | Y+Z / -- | M | IB |
| R5 | |||||||||||||
| 23S | 131:148 | 125:129 | U:A (WC) | a:u (44.7%), g:c (41.6%) | CUA | - (100%) | 10.74 | 5' | A | 3??33/????? | None / -- | M | IB |
| 23S | 1565:1568 | 1651:1655 | C:G (WC) | C:G (94.6%) | CAU | CDU (100%)* | 10.52 | 5' | A | 32223/bumMb | None / L2, L37ae | M | IB |
| (Class III) | |||||||||||||
| 16S | 64:68 | 64:68 | G:G (H) | G:G (78.1%), u:u (14.6%) | UGC | ARC (70.7%) | 11.49 | 5',3' | P | 32333/MmMMM | Y+Z+L / -- | I | III |
| 16S | 934:938 | 911:915 | C:A (rWb) | C:A (96.0%) | ACA | ACA (83.0%) | 11.39 | 3' | P | 23333/mmmmm | X+Y+Z / -- | M | III |
| 16S | 1053:1057 | 1035:1039 | G:G (H) | G:G (99.4%) | CAU | CAU (96.8%) | 11.31 | 5',3' | P | 23333/mmmmm | Y+Z+L / S3 | I | III |
- E. coli-equivalent position numbers for the lonepair of the lonepair triloop.
- Nucleotide numbers of lonepairs present in the crystal structures of the T. thermophilus 30 S subunit (PDB entry 1FJF),10 H. marismortui 50 S subunit (PDB entry 1JJ2),12 and S. cerevisiae Phe-tRNA (PDB entry 6TNA).38
- Lonepair types and conformations in the crystal structures: WC, Watson-Crick; rWC, reversed Watson-Crick; Wb, Wobble; rWb, reversed Wobble; H, Hoogsteen; rH, reversed Hoogsteen; S, sheared; NC, other non-canonical (see also Fig. 5).
- Comparative information for lonepairs and triloops in the nuclear encoded rRNA genes in the three phylogenetic domains for rRNAs and Type 1 tRNAs for tRNAs. The dominant (more than 50% conserved) sequences are in uppercase and the minor (10-50% conserved) sequences in lowercase. The IUPAC-IBC nomenclature for nucleotides was utilized72. The asterisk (*) represents the triloop sequence in archaea.
- Triloop sequences in the crystal structures.
- dCC: the distances in Angstroms between the two C1' atoms in the lonepairs in the crystal structures.
- lpS: lonepair stacking onto its closest 5'- and/or 3'-helices.
- D: directionality of the two local chains involved in a lonepair: A, antiparallel; P, parallel.
- sp/bf: sugar puckering/bases facing into for each of the five nucleotides in the lonepair triloop motif. Sugar puckering: 3, C3'-endo; 2, C2'-endo. Bases facing into: M, major groove; m, minor groove; b, major-minor groove boundary; u, straight up the backbone.
- TI: LPTL tertiary interactions: X, Y and Z indicate the first, second, and third nucleotides in the triloop, respectively. Interactions with ribosomal proteins, when present, are indicated in square brackets.
- L: Loop type. H, hairpin; I, internal; M, multistem.
- C: Classification of lonepair triloop. See Classification of lonepair triloops in the text and Fig. 2.
