Table of Results

Last modified on 22 May 2000.

Crosslinking information:

Crosslinking references are shown only in support of comparative sequence analysis observations.
References were collected from the Database of Ribosomal Crosslinks (DRC). Interested visitors should browse their web site.
Reference links point to Entrez PubMed at the National Center for Biotechnology Information (NCBI).
For each crosslink reference, a direct link to the DRC page containing that reference is also provided, as [DRC-molecule].

All position numbering is done using the *E. coli* structure model reference sequence numbering system. LT = "Loop Type," where H = hairpin, I = internal, M = multi-stem, and PK = pseudoknot. LC = "Loop Coordinates," indicating the range of nucleotides included in the loop. **UTP** = "U-Turn Position," where the first nucleotide of the loop = 1. **FBP** = "Flanking Basepair Position;" cases where no flanking pair is proposed are indicated with "Unknown." Experimental interactions which are not included in the comparative model are shown in red. Speculative interactions which are not included in the comparative models are shown in *italics*. Pairs which also close a hairpin loop are shown in **bold**. TC = Comparative Structure Model "Tertiary Coordinates," in the format (position relative to turn):(tertiary). Tertiary interactions occuring in the "favored region" (nucleotides -1 through +3) are shown in **bold**. Tentative tertiary interactions are shown in *italics*. References selected from the "Notes" column will appear in a separate window. Full details of the comparative structure models are available at the Comparative RNA Web Site.
Category	rRNA	LT	LC	UTP	FBP	TC	Notes
A: Canonical GNRA hairpin loops	16S	H	159-162	1	158:163	NONE
	16S	H	297-300	1	296:301	NONE
	16S	H	727-730	1	726:731	NONE	Crystal structure: Agalarov et al. Science 288:107 (2000).
	16S	H	898-901	1	897:902	NONE
	16S	H	1077-1080	1	1076:1081	NONE
	16S	H	1266-1269	1	1265:1270	NONE
	23S	H	463-466	1	462:467	NONE
	23S	H	630-633	1	629:634	NONE
	23S	H	1223-1226	1	1222:1227	NONE
	23S	H	2375-2378	1	2374:2378	NONE
	23S	H	2595-2598	1	2594:2599	NONE
	23S	H	2659-2662	1	2658:2663	*+2: [2661(2550:2558)]*	Crystal structure: Szewczak and Moore J. Mol. Biol. 247:81 (1995). Crystal structure: Correll et al. Proc. Natl. Acad. Sci. USA 95:13436 (1998). Crystal structure: Ban et al. Nature 400:841 (1999).
	23S	H	2857-2860	1	2856:2861	NONE
B: GNRA in larger hairpin loops	16S	H	1315-1322	2	Unknown	NONE
	23S	H	306-311	2	306:311	NONE
	23S	H	745-752	4	Unknown	-2: [746(2057:2611)]	Crosslink: Stiege et al. Nucleic Acids Res. 11:1687 (1983). Crosslink: Stiege et al. J. Mol. Biol. 191:135 (1986). [DRC-23S]
	23S	H	780-784	1	779:785	NONE
C: GNRA in non-hairpin loops	16S	M	765-768	1	577:764	NONE
	16S	M	1108-1112	1	1068:1107	+1: [1109(933:1384)]
	23S	M	215-223	6	*	-1: [219(234:430)] +1: [221(265:427)]	* Nucleotide -1 is part of the base triple [219(234:430)] rather than a base pair.
	23S	M	475-483	2	Unknown	NONE
	23S	I	511-515	2	Unknown	NONE
	23S	M	818-821	1	817:1190	NONE
	23S	I	1565-1572	4	Unknown	NONE
	23S	M	1668-1681	7	Unknown	NONE
D: UNR in trinucleotide hairpin loops	23S	H	1083-1085	1	1082:1086	+1: [1084(1054:1105)] +2: [1085(1055:1104)]	See Table 2. Crystal structure: Conn et al. Science 284:1171 (1999). Crystal structure: Wimberly et al. Cell 97:491 (1999).
D: UNR in trinucleotide hairpin loops	23S	H	1926-1928	1	1925:1929	*+2: (1834:1928)*	See Table 2.
E: UNR at position 2 in hairpin loops flanked by Y:H basepairs	16S	PK	13-16	2	13:21	-1: (13:920) 0: (14:1398) +1: (15:1397) +2: (16:920)
	16S	H	322-331	2	Unknown	NONE
	16S	H	618-622	2	618:622	NONE	618:622 was included in an earlier version of the comparative structure model: Gutell R.R. (1996). Comparative Sequence Analysis and the Structure of 16S and 23S rRNA. In: Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis. pp. 111-128. Dahlberg A. and Zimmerman B. (eds.) CRC Press. Boca Raton.
	16S	H	1090-1095	2	Unknown	NONE
	23S	H	567-574	2	Unknown	+6: (574:2034)	Crosslink: Stiege et al. Nucleic Acids Res. 11:1687 (1983). Crosslink: Stiege et al. J. Mol. Biol. 191:135 (1986). [DRC-23S]
	23S	H	1065-1073	2	Unknown	+5: [1071(1091:1100)] +6: [1072(1092:1099)]	Comparative: Conn et al. Biochemistry37:11980 (1998). Crystal structure: Conn et al. Science 284:1171 (1999). Crystal structure: Wimberly et al. Cell 97:491 (1999).
F: UNR in hairpin loops flanked by G:A basepairs	16S	H	260-266	2	Unknown	NONE
	16S	H	691-696	2	690:697	NONE	Moazed & Noller Nature 342:142 (1989). Powers et al. J. Mol. Biol. 232:362 (1993). Merryman et al. J. Mol. Biol. 285:97 (1999).
	23S	H	714-717	1	713:718	NONE	See Table 3: (713:718) closing base pair story (eub GA; euk/arc Watson-Crick). Crystal structure: Culver et al. Science 285:2133 (1999).
	23S	H	1093-1098	2	1093:1098	NONE	NMR structure: Huang et al. J. Mol. Biol. 258:308 (1996). NMR structure: Fountain et al. Biochemistry 35:6539 (1996). Crystal structure: Conn et al. Science 284:1171 (1999). Crystal structure: Wimberly et al. Cell 97:491 (1999).
G: UNR in non-hairpin loops flanked by C:G basepairs	16S	M	1211-1214	1	1047:1210	NONE
	23S	I	1352-1354	1	1351:1380	NONE
	23S	M	2197-2199	1	2093:2196	NONE
H: UNR in loops flanked by other basepairs	16S	H	787-795	3	Unknown	NONE	Similar to T(Psi)U loop in tRNA: Gu et al. Biochemistry 33:2255 (1994). Lee et al. J. Mol. Biol. 269:732 (1997). Powers et al. J. Mol. Biol. 232:362 (1993). Merryman et al. J. Mol. Biol. 285:97 (1999).
	16S	M	1065-1067	1	1064:1192	NONE
	16S	H	1358-1364	1	1357:1365	NONE	eub (AG, GA); arc/euk (Watson-Crick)
	23S	H	1951-1955	1	1950:1956	+3: [1954(1950:1956)]
	23S	I	2738-2741	2	Unknown	NONE
I: UNR in loops without flanking basepairs	16S	M	116-121	3	Unknown	0: (118:288) +1: (119:287) +3: [121(124:237)(125:236)]	Babin et al. RNA 5:1430 (1999). Crosslink: Stiege et al. J. Mol. Biol. 191:135 (1986). [DRC-16S]
	16S	M	557-566	5	Unknown	+5: (566:919)
	23S	M	446-460	3	Unknown	NONE
	23S	M	1339-1342	2	Unknown	+3: (1343:1404) +4: (1344:1403)	Experimental support: Kooi et al. Proc. Natl. Acad. Sci. USA 90:213 (1993).
	23S	I	2162-2173	6	Unknown	+2: (2112:2169) +3: (2113:2170) +5: (2117:2172)	Covariation: support for (2112:2169), (2113:2170), and (2117:2172). AA,AG@helix.ends: (2125:2173) and (2126:2162); therefore, loop boundaries are 2163-2172. Moazed & Noller Cell 57:585 (1989). Crosslink (all three): Doring et al. Nucleic Acids Res. 19:3517 (1991). [DRC-23S]
	23S	H	2265-2275	8	Unknown	*0: (2272:2564)*
	23S	M	2422-2433	2	Unknown	-2: [(2420:2396)2180] +4: (2427:2282) +5: (2428:2359)	Crosslink (2427:2282): Stiege et al. J. Mol. Biol. 191:135 (1986). [DRC-23S]
	23S	M	2448-2454	2	Unknown	+4: (2453:2499) +5: (2454:2498)
	23S	M	2497-2506	4	Unknown	-2: (2498:2454) -1: (2499:2453) +4: (2504:2447) and [(2504:2447)2508]
	23S	M	2583-2587	3	Unknown	+1: (2586:1782)	Crosslink: Stiege et al. Nucleic Acids Res. 11:1687 (1983). [DRC-23S]
J: Ambigous UNR/GNRA exchanges	16S	H	863-866	1	862:867	0: [863(570:866)] +2: (865:571) +3: (866:570)	Support for (570:866) and (571:865): Covariation: Gutell et al. EMBO J 5:1111 (1986). Experimental: Vila et al. Proc. Natl. Acad. Sci. USA 91:11148 (1994).
J: Ambigous UNR/GNRA exchanges	16S	H	1013-1016	1	1012:1017	*0, +3: (1013:1016)*

Comparative RNA Web Site and Project The Gutell Lab

Table of Results