Table 3.
Structural motifs used for the Bacillus anthracis tmRNA mode
| Motif | SCOR class | tmRNA Res. | Source Res. | Coordinates | Comments |
| 1 | 1–11, 12–27, 316–355 | 1–11, 13–28, 324–363 | E. coli 1 | ACCA end and G3-U349 pair | |
| 2 | loop with stacked interdigitated bases | 28–33, 312–316 | 477–482, 451–455 | 1J5E.pdb | |
| 3 | 300–301 | ERNA-3D | |||
| 4a | 43–53, 61–65, 294–299 | 43–53, 63–67, 302–308 | E. coli model | helix 2d, helix 3 | |
| 4b | pseudoknot | 58–60, 66, 67–73 | 12–14, 20, 23–29, | 1RNK.pdb | pk1, helix 4b |
| 4c | 54–56, 74–75 | 54–56, 77–78 | E. coli 6a | pk1, helix 4a | |
| 5 | heptaloop | 82–88 | 335–341 | 1JJ2.pdb | |
| 6a | one looped out A | A112 | 210 | 1GID.pdb | |
| 6b | C114, C127 | ERNA-3D | |||
| 6c | octaloop | 117–124 | 1499–1506 | 1JJ2.pdb | |
| 7a | 134–138, U163, A164, 165–169, | 140–144, A171, A174, 175–179 | E. coli 10b | helix 6a, looped out U163 and A164. | |
| 7b | one looped out U | U158 | U87 | 1JJ2.pdb | |
| 7c | 144–147, 148–156, 180–185 | 259–262, 264–272, 293–298 | E. coli 13b | helix 6c, helix 7, pk2 | |
| 8 | G133, C170, 171–177, 178–179 | C138, G181, 182–188, 190–191 | E. coli 10b | ||
| 9a | C190, 191–198, 208–215, 216 | G200, 203–210, 219–226, U229 | E. coli 11a, 11b | purine-rich loop, pk3 | |
| 9b | pseudoknot | 202–206, 228–232 | 9–13, 28–32 | 1RNK.pdb | pk3, helix 9 |
| 10a | 199–201 | 154–156 | E. coli 6a | pk3 | |
| 10b | 217–227 | 229–239 | E. coli 6a | pk3 | |
| 11a | one looped out C | C269 | C6 | 1BVJ.pdb | |
| 11b | stacked duplexes with four non-WC pairs | 241–245, 260–263 | 795–798, 815–818 | 1JJ2.pdb | |
| 12 | 246–259, 275–290 | 259–277, 284–299 | E. coli 6a | helix 10c, helix 11ab, pk4 |
Motif numbers in bold, their SCOR classification [12], residue positions in the tmRNA model and the source structure are shown in columns one to four. Column five lists the filenames containing the atomic coordinates that were derived from the PDB [31], the E. coli model (see Table 2), or were generated by ERNA-3D [11].