Comparative 3-D Modeling of tmRNA

BMC Molecular Biology

Table 2 Structural motifs used for the Escherichia coli tmRNA model

Motif	SCOR class	tmRNA Res.	Source Res.	Coordinates	Comments
1		1–7, 353–363	1–7, 12–22	1IKD.pdb (chain W)	ACCA end and G3-U357 pair
2		8–28, 325–352	8–28, 325–352	tmx-34.pdb from tmRDB
3a	internal loop with unpaired stacked bases	29–33, 321–324	1775–1779, 1765–1768	1JJ2.pdb
3b	stacked duplex with one non-WC pair	C35, A319		ERNA-3D
4	stacked duplex with two non-WC pairs	38–39, 315–316	2874–2875, 2882–2883	1JJ2.pdb
5		309–311		ERNA-3D
6a	pseudoknot	49–78	1–33	1RNK.pdb	pk1
6b	tetraloop	87–98	5–8	1AFX.pdb	the only YRRR tetraloop in SCOR
7	nonaloop	118–126	1834–1842	1JJ2.pdb
8	one unpaired and stacked U	U131	U30	1B36.pdb
9		171–174		ERNA-3D
10a	stacked duplex with two non-WC pairs	149–150, 165–166	288–289, 363–364	1JJ2.pdb
10b	pseudoknot	138–196		6a	pk2
11a	internal loop	204–206, 223–225	780–782, 800–802	1J5E.pdb
11b	pseudoknot	197–247		6a	pk3
12	stacked duplex with one non-WC pair	G258, A273	A-G6, B-A27	420D.pdb
13a	stacked duplex with one non-WC pair	C266, U296		ERNA-3D
13b	pseudoknot	248–299		6a	pk4

Shown in columns one to four are the motif numbers in bold, their SCOR classification [12], the residue positions in the tmRNA model and the source structure. column five lists the filenames containing the atomic coordinates that were derived from the PDB [31], the tmRDB [52], or were generated by ERNA-3D [11].

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