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].