Comparative 3-D Modeling of tmRNA

Table 4 Structural motifs used for the Caulobacter crescentus tmRNA model

Motif	SCOR class	tmRNA Res.	Source Res.	Coordinates	Comments
1		A-1-13, A-14-21, B-50-83	1–13, 15–22, 322–355.	B. anthracis 1	-
2a	one non-Watson Crick pair and one looped-out A	A-22, B-48-49	14, 4–5	5MSF.pdb	disruption in anticodon stem
2b	loop with base triple	A-26-31; B-40-44	8–13, 24–28	1FMN.pdb
2c		A-C36, B-C35		ERNA-3D
3		A-40-41, B-27-31		ERNA-3D
4		A-47-61, A-62-70	196–210, 224–232	B. anthracis 8a, 8b, 9a, 9c	pk1
5		A-87-93	82–88	B. anthracis 5	terminal heptaloop of helix m2
6	one looped out A and one or more non-WC pairs	A-78-81, A-99-101	113–116, 205–207	1GID.pdb	internal loop between helices m1 and m2
7		B-8-11	284–285, 291–292	1D6K.pdb
8a		A-112-114, A-131-132		ERNA-3D
8b		A-119-125	82–88	B. anthracis 5
9a		U148, C163		ERNA-3D
9b		A-156-165, A-146-153, A-167-171	157–166, 149–156, 192–196	E. coli 10b	pk2. Single-stranded regions were adjusted to connect helices
10		A-154-156, A-170-171	54–55, 76–77	E. coli 6a	Correction of two pairs in pk2 based on E. coli pk1
11		A-211-214, A-177-182, A-184-193, A-177-178, A-192-198, A-194-209	360–363, 207–212, 213–222, 200–201, 228–234, 230–245	E. coli 1 (ACCU tail) and 11b	pk3 and ACCU tail of pk3

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 or B. anthracis models (see Tables 2 and 3), or were generated by ERNA-3D [11].