Table 3 Structural motifs used for the Bacillus anthracis tmRNA mode

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