Annotating tertiary motifs in RNA structures

1VQO - 50S ribosomal subunit

Statistics of tertiary motifs

Annotated diagram (PDF, EPS)

Structure information of tertiary motifs

• Coaxial helix

ID	Strand 1		Strand 2
	Seq num	Chain	Seq num	Chain
1	12-29,32-41	0	440-441,443-448,450-451,479-480,516-531	0
2	152-164	0	171-174,176-182,184-185	0
3	60-62,64-66,109-112,131-136	0	49-55,84-86,142-147	0
4	190-191,223-224,227-233,237-239,241-242,244-245	0	206-212,216-217,266-267,269-270,431-435	0
5	369-374,376-377,412-416,2444-2459	0	273-280,418-428,2432-2436,2438-2442	0
6	286-293,295-304,332-334	0	342-344,347-356,359-366	0
7	309-312,340-341	0	319-322,324-325	0
8	539-548,555-563	0	594-602,608-617	0
9	566-569,571-576	0	581-586,589-592	0
10	632-635,2060-2061	0	620-623,2075-2076	0
11	1360-1368	0	636-641,2056-2058	0
12	762-774	0	887-893,895-896,899-902	0
13	661-664,666-670	0	676-680,682-686	0
14	716-726,728-733	0	702-712,738-743	0
15	808-819,821-823,827-830,832-834,836-837	0	791-805,846-854	0
16	924-939	0	915-919,1031-1041	0
17	940-942,944-952,954-958,963-969	0	999-1005,1008-1009,1011-1013,1015-1025	0
18	1132-1136,1138-1147	0	1216-1230	0
19	1151-1152,1155-1160,1194-1197	0	1202-1205,1207-1215	0
20	1248-1258,1261-1276	0	1089-1095,1098-1101,1110-1115,1280-1286,1289-1290	0
21	1060-1071,1293-1312	0	905-914,1045-1054,1342-1351,1353-1354	0
22	1395-1404,1703-1707	0	1383-1387,1711-1715,1718-1721	0
23	1420-1425,1429-1430	0	1436-1437,1439-1444	0
24	1507-1521	0	1449-1450,1494-1498,1665-1672	0
25	1454-1456,1459-1468	0	1474-1475,1477-1484,1489-1491	0
26	1561-1562,1564-1569,1634-1639,1641-1650	0	1535-1544,1546-1557,2738-2739	0
27	1618-1624,1626-1629	0	1570-1578,1632-1633	0
28	1372-1374,1725-1728	0	2047-2053	0
29	1760-1765,1767-1770	0	1773-1776,1779-1784	0
30	1820-1828	0	2020-2021,2023-2029	0
31	2623-2630	0	2633-2636,2638-2641	0
32	1855-1856,1858-1863	0	1866-1871,1873-1874	0
33	1931-1939,1942-1946	0	1891-1893,1896-1902,1905-1908	0
34	1964-1967	0	1947-1948,1969-1970	0
35	2650-2660	0	2084-2091,2093-2095	0
36	2260-2270,2272-2276,2470-2473,2476-2481	0	2105-2108,2110-2115,2118-2133	0
37	2239-2241,2244-2249	0	2134-2136,2252-2257	0
38	2306-2307,2310-2315	0	2293-2298,2300-2301	0
39	2357-2358,2422-2424	0	2362-2366	0
40	2398-2407,2409-2412	0	2381-2390,2415-2418	0
41	2490-2492,2494-2507	0	2513-2524,2527-2531	0
42	2543-2552,2555-2563	0	2570-2575,2578-2580,2602-2606,2609-2610,2613-2615	0
43	2700-2717,2721-2725,2727-2737	0	2682-2691,2693-2695,2742-2746,2750-2755,2757-2761,2763-2767	0
44	2667-2672,2675-2679	0	2806-2810,2817-2822	0
45	2769-2773,2776-2780,2783-2785	0	2787-2789,2793-2798,2801-2805	0
46	2827-2836	0	2844-2848,2909-2914	0
47	2853-2865	0	2891-2895,2897-2901,2903-2905	0
48	2868-2877	0	2880-2889	0
49	3027-3033,3038-3039	9	3044-3045,3047-3050,3053-3055	9
50	3059-3064,3066-3067,3069-3077,3079-3086,3088-3090	9	3014-3021,3093-3112	9



• A-minor

ID	Residue 1			Residue 2			Residue 3
	Seq	Seq num	Chain	Seq	Seq num	Chain	Seq	Seq num	Chain
1	A	1107	0	G	1100	0	C	1256	0
2	A	1630	0	G	1555	0	C	1566	0
3	A	2361	0	G	2295	0	C	2313	0
4	A	665	0	C	230	0	G	209	0
5	A	2681	0	G	2713	0	C	2767	0
6	A	2010	0	C	1889	0	G	2013	0
7	A	242	0	G	273	0	C	377	0
8	A	666	0	G	231	0	C	208	0
9	A	1572	0	G	1510	0	C	1495	0
10	A	449	0	G	1349	0	C	1305	0
11	A	2883	0	G	1806	0	C	1786	0
12	A	2776	0	C	2559	0	G	2574	0
13	A	1079	0	G	2068	0	C	2077	0
14	A	1082	0	G	1046	0	C	1068	0
15	A	552	0	G	1323	0	C	1334	0
16	A	1470	0	C	179	0	G	157	0
17	A	2727	0	C	2895	0	G	2861	0
18	A	1132	0	G	2522	0	C	2498	0
19	A	520	0	G	1363	0	C	638	0
20	A	521	0	G	1364	0	C	637	0
21	A	532	0	G	2660	0	C	2084	0
22	A	1375	0	C	1735	0	G	2044	0
23	A	305	0	C	330	0	G	326	0
24	A	2875	0	C	1787	0	G	1805	0
25	A	551	0	G	1322	0	C	1335	0
26	A	2425	0	G	2314	0	C	2294	0
27	A	69	0	G	54	0	C	65	0
28	A	2906	0	G	2847	0	C	2833	0
29	A	1632	0	G	1568	0	C	1553	0
30	A	1581	0	G	1540	0	U	1645	0
31	A	1941	0	A	1881	0	U	1850	0
32	A	1997	0	C	2026	0	G	1823	0
33	A	1007	0	A	2311	0	U	2297	0
34	A	243	0	G	274	0	C	376	0
35	A	1152	0	G	1216	0	C	1147	0
36	A	767	0	G	2110	0	C	2477	0
37	A	1616	0	G	1542	0	C	1643	0
38	A	1492	0	G	1672	0	C	1514	0
39	A	2600	0	G	2580	0	C	2555	0
40	A	1994	0	G	2584	0	C	2594	0
41	A	1493	0	G	1449	0	C	1513	0
42	A	1659	0	G	1490	0	C	1455	0
43	A	737	0	G	2383	0	C	2405	0
44	A	565	0	A	1092	0	U	1264	0
45	A	682	0	G	209	0	C	230	0
46	A	1097	0	G	1074	0	C	1085	0
47	A	580	0	C	1253	0	G	1110	0
48	A	193	0	G	413	0	C	427	0
49	A	566	0	G	1093	0	C	1263	0
50	A	1969	0	G	1945	0	C	1892	0
51	A	1098	0	G	1075	0	C	1084	0
52	A	161	0	G	892	0	C	769	0
53	A	1132	0	U	2499	0	A	2521	0
54	A	698	0	G	742	0	C	729	0
55	A	2307	0	G	1052	0	U	1062	0
56	A	472	0	U	888	0	A	773	0
57	A	1330	0	G	1300	0	C	905	0
58	A	2633	0	G	2471	0	C	2114	0
59	A	519	0	A	639	0	U	1362	0
60	A	1458	0	U	862	0	A	784	0
61	A	643	0	G	902	0	C	762	0
62	A	2905	0	G	2834	0	C	2846	0
63	A	1058	0	C	2530	0	G	2491	0
64	A	1693	0	C	847	0	G	836	0
65	A	1381	0	G	1401	0	C	1721	0
66	A	2775	0	G	2558	0	C	2575	0
67	A	2599	0	G	2579	0	C	2556	0
68	A	152	0	G	41	0	C	440	0
69	A	439	0	G	184	0	C	153	0
70	A	1106	0	G	1099	0	C	1257	0
71	A	1615	0	G	1541	0	C	1644	0
72	A	1188	0	G	1158	0	C	1209	0
73	A	1081	0	G	1045	0	C	1069	0
74	A	160	0	G	891	0	C	770	0
75	A	736	0	A	2382	0	U	2406	0
76	A	536	0	G	2075	0	C	2061	0
77	A	1078	0	A	2067	0	U	2078	0
78	A	1317	0	G	1312	0	C	1342	0
79	A	1133	0	C	2500	0	G	2520	0
80	A	1486	0	G	1453	0	C	1674	0
81	A	1658	0	G	1489	0	C	1456	0
82	A	602	0	G	554	0	C	605	0
83	A	306	0	A	340	0	U	325	0
84	A	1296	0	G	1038	0	U	932	0
85	A	1930	0	A	2266	0	U	2127	0
86	A	1318	0	A	516	0	U	27	0
87	A	48	0	A	148	0	U	43	0
88	A	187	0	G	182	0	C	154	0
89	A	1501	0	G	1443	0	C	1421	0
90	A	1858	0	G	1877	0	C	1854	0
91	A	1866	0	G	1475	0	C	1467	0
92	A	1476	0	C	1862	0	G	1867	0
93	A	1968	0	G	1944	0	C	1893	0
94	A	1909	0	U	2127	0	A	2266	0
95	A	1631	0	A	1567	0	U	1554	0
96	A	2062	0	G	2094	0	C	2651	0
97	A	1459	0	G	863	0	C	783	0
98	A	693	0	G	2452	0	C	2440	0
99	A	2362	0	G	2312	0	C	2296	0
100	A	1842	0	C	2021	0	G	1827	0
101	A	1931	0	G	2267	0	C	2126	0
102	A	1040	0	C	910	0	G	1295	0
103	A	874	0	G	1832	0	C	1844	0
104	A	2827	0	G	2667	0	C	2822	0
105	A	2566	0	G	2700	0	C	2695	0
106	A	1057	0	G	2529	0	U	2492	0
107	A	1233	0	A	2604	0	U	2550	0
108	A	455	0	G	32	0	C	451	0
109	A	2395	0	A	916	0	U	927	0
110	A	3080	9	C	1011	0	G	956	0
111	A	2840	0	G	1728	0	C	2047	0
112	A	1865	0	C	1474	0	G	1468	0
113	A	3104	9	U	1009	0	A	957	0
114	A	1006	0	G	2310	0	C	2298	0
115	A	99	0	C	93	0	G	81	0
116	A	1471	0	C	156	0	G	180	0



• Ribose zipper

ID	Strand 1			Strand 2
	Seq	Seq num	Chain	Seq	Seq num	Chain
1	5′-AA-3′	160,161	0	5′-CC-3′	769,770	0
2	5′-UG-3′	1062,1063	0	5′-UA-3′	2306,2307	0
3	5′-AA-3′	1097,1098	0	5′-CC-3′	1084,1085	0
4	5′-AA-3′	1968,1969	0	5′-CC-3′	1892,1893	0
5	5′-AA-3′	565,566	0	5′-CU-3′	1263,1264	0
6	5′-AA-3′	520,521	0	5′-CC-3′	637,638	0
7	5′-AA-3′	2775,2776	0	5′-GC-3′	2574,2575	0
8	5′-AA-3′	665,666	0	5′-CG-3′	208,209	0
9	5′-AA-3′	1858,1859	0	5′-CC-3′	1853,1854	0
10	5′-AA-3′	1930,1931	0	5′-CU-3′	2126,2127	0
11	5′-AA-3′	1631,1632	0	5′-CU-3′	1553,1554	0
12	5′-AA-3′	1615,1616	0	5′-CC-3′	1643,1644	0
13	5′-AA-3′	1006,1007	0	5′-UC-3′	2297,2298	0
14	5′-AA-3′	2599,2600	0	5′-CC-3′	2555,2556	0
15	5′-AG-3′	1318,1319	0	5′-UU-3′	26,27	0
16	5′-AA-3′	242,243	0	5′-CC-3′	376,377	0
17	5′-AA-3′	1865,1866	0	5′-CG-3′	1467,1468	0
18	5′-AA-3′	1658,1659	0	5′-CC-3′	1455,1456	0
19	5′-AA-3′	736,737	0	5′-CU-3′	2405,2406	0
20	5′-GU-3′	2491,2492	0	5′-AA-3′	1057,1058	0
21	5′-GA-3′	471,472	0	5′-AC-3′	773,774	0
22	5′-AC-3′	152,153	0	5′-AC-3′	439,440	0
23	5′-AA-3′	1078,1079	0	5′-CU-3′	2077,2078	0
24	5′-AA-3′	551,552	0	5′-CC-3′	1334,1335	0
25	5′-AA-3′	1081,1082	0	5′-CC-3′	1068,1069	0
26	5′-CA-3′	1993,1994	0	5′-CU-3′	2594,2595	0
27	5′-GA-3′	2632,2633	0	5′-CU-3′	2114,2115	0
28	5′-GA-3′	579,580	0	5′-GU-3′	1110,1111	0
29	5′-AU-3′	204,205	0	5′-AG-3′	189,190	0
30	5′-AA-3′	1458,1459	0	5′-CA-3′	783,784	0
31	5′-AA-3′	1132,1133	0	5′-GA-3′	2520,2521	0
32	5′-UA-3′	233,234	0	5′-AA-3′	436,437	0
33	5′-AA-3′	1106,1107	0	5′-CC-3′	1256,1257	0
34	5′-AA-3′	790,791	0	5′-CG-3′	1708,1709	0
35	5′-AA-3′	1492,1493	0	5′-CC-3′	1513,1514	0
36	5′-AA-3′	1329,1330	0	5′-CC-3′	905,906	0
37	5′-AA-3′	305,306	0	5′-UG-3′	325,326	0
38	5′-CU-3′	1456,1457	0	5′-AA-3′	1657,1658	0
39	5′-GG-3′	2642,2643	0	5′-UA-3′	1838,1839	0
40	5′-AG-3′	1294,1295	0	5′-AU-3′	1040,1041	0
41	5′-CG-3′	2822,2823	0	5′-GA-3′	2826,2827	0
42	5′-CG-3′	729,730	0	5′-GA-3′	697,698	0
43	5′-GC-3′	2558,2559	0	5′-GA-3′	2798,2799	0
44	5′-GG-3′	2862,2863	0	5′-GU-3′	2755,2756	0
45	5′-CC-3′	930,931	0	5′-GA-3′	911,912	0
46	5′-AA-3′	1188,1189	0	5′-CC-3′	1208,1209	0
47	5′-CC-3′	1786,1787	0	5′-GA-3′	2882,2883	0
48	5′-AG-3′	955,956	0	5′-AC-3′	3080,3081	0
49	5′-AA-3′	1012,1013	0	5′-GA-3′	3102,3103	0



• Pseudoknot

ID	Seq num	Chain
1	314-315,324-325,336-337,340-341	0
2	309-312,314-315,319-322,336-337	0
3	2357-2358,2422-2424,2362-2366	0
4	1449-1450,1451-1453,1673-1675,1512-1513	0
5	1102-1104,1121-1122,1239-1243	0
6	2060-2061,2064-2068,2075-2081	0
7	324-325,332-334,340-344	0
8	314-315,332-334,336-337,342-344	0



• Loop-loop receptor

ID	Loop		Receptor
	Seq num	Chain	Seq num	Chain
1	469-472	0	771-774,887-890	0
2	1055-1058	0	2489-2494,2527-2531	0
3	2630-2633	0	2113-2116,2469-2472	0
4	735-738	0	2381-2384,2404-2407	0
5	1629-1632	0	1552-1555,1565-1568	0
6	1966-1969	0	1891-1894,1943-1946	0



• Kissing hairpin

ID	Strand 1		Strand 2
	Seq num	Chain	Seq num	Chain
1	1560-1561	0	2738-2739	0
2	57-58	0	88-89	0
3	418-423	0	2444-2449	0