BMRB: 34796

Integrated NMR/MD structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop

Authors

Oxenfarth, A., Kuemmerer, F., Bottaro, S., Schnieders, R., Pinter, G., Jonker, H.R.A., Fuertig, B., Richter, C., Blackledge, M., Lindorff-Larsen, K., Schwalbe, H.

Assembly

RNA hairpin with CUUG tetraloop

Entity

1. RNA hairpin with CUUG tetraloop (polymer, Thiol state: not present), 14 monomers, 4517.655 Da Detail

GGCAGCUUGC UGCC

Formula weight

4517.655 Da

Source organism

synthetic RNA

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 122, ¹³C: 93, ¹⁵N: 10, ³¹P: 13 assignments Detail

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ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	G	H1'	H	5.84	0.01	1
2	1	1	G	H2'	H	4.96	0.01	1
3	1	1	G	H3'	H	4.72	0.01	1
4	1	1	G	H4'	H	4.58	0.01	1
5	1	1	G	H5'	H	4.43	0.01	2
6	1	1	G	H5''	H	4.30	0.01	2
7	1	1	G	H8	H	8.13	0.01	1
8	1	1	G	C1'	C	91.38	0.01	1
9	1	1	G	C2'	C	75.10	0.01	1
10	1	1	G	C3'	C	74.98	0.01	1
11	1	1	G	C4'	C	83.53	0.01	1
12	1	1	G	C5'	C	67.61	0.01	1
13	1	1	G	C8	C	139.03	0.01	1
14	1	2	G	H1	H	13.26	0.01	1
15	1	2	G	H1'	H	5.92	0.01	1
16	1	2	G	H2'	H	4.59	0.01	1
17	1	2	G	H3'	H	4.56	0.01	1
18	1	2	G	H4'	H	4.56	0.01	1
19	1	2	G	H5'	H	4.51	0.01	2
20	1	2	G	H5''	H	4.29	0.01	2
21	1	2	G	H8	H	7.59	0.01	1
22	1	2	G	C1'	C	93.10	0.01	1
23	1	2	G	C2'	C	75.37	0.01	1
24	1	2	G	C3'	C	73.27	0.01	1
25	1	2	G	C4'	C	82.65	0.01	1
26	1	2	G	C5'	C	66.40	0.01	1
27	1	2	G	C8	C	136.81	0.01	1
28	1	2	G	N1	N	148.54	0.01	1
29	1	2	G	P	P	-0.41	0.01	1
30	1	3	C	H1'	H	5.53	0.01	1
31	1	3	C	H2'	H	4.59	0.01	1
32	1	3	C	H3'	H	4.56	0.01	1
33	1	3	C	H4'	H	4.45	0.01	1
34	1	3	C	H5	H	5.30	0.01	1
35	1	3	C	H5'	H	4.58	0.01	2
36	1	3	C	H5''	H	4.14	0.01	2
37	1	3	C	H6	H	7.68	0.01	1
38	1	3	C	H41	H	8.46	0.01	1
39	1	3	C	H42	H	6.81	0.01	1
40	1	3	C	C1'	C	93.91	0.01	1
41	1	3	C	C2'	C	75.48	0.01	1
42	1	3	C	C3'	C	72.35	0.01	1
43	1	3	C	C4'	C	81.94	0.01	1
44	1	3	C	C5	C	97.45	0.01	1
45	1	3	C	C5'	C	64.65	0.01	1
46	1	3	C	C6	C	140.84	0.01	1
47	1	3	C	N4	N	97.78	0.01	1
48	1	3	C	P	P	-0.99	0.01	1
49	1	4	A	H1'	H	5.90	0.01	1
50	1	4	A	H2	H	7.01	0.01	1
51	1	4	A	H2'	H	4.52	0.01	1
52	1	4	A	H3'	H	4.72	0.01	1
53	1	4	A	H4'	H	4.52	0.01	1
54	1	4	A	H5'	H	4.56	0.01	2
55	1	4	A	H5''	H	4.18	0.01	2
56	1	4	A	H8	H	7.95	0.01	1
57	1	4	A	C1'	C	93.35	0.01	1
58	1	4	A	C2	C	152.40	0.01	1
59	1	4	A	C2'	C	75.59	0.01	1
60	1	4	A	C3'	C	73.03	0.01	1
61	1	4	A	C4'	C	82.11	0.01	1
62	1	4	A	C5'	C	65.46	0.01	1
63	1	4	A	C8	C	139.43	0.01	1
64	1	4	A	P	P	-0.50	0.01	1
65	1	5	G	H1	H	13.11	0.01	1
66	1	5	G	H1'	H	5.70	0.01	1
67	1	5	G	H2'	H	4.09	0.01	1
68	1	5	G	H3'	H	4.62	0.01	1
69	1	5	G	H4'	H	4.37	0.01	1
70	1	5	G	H5'	H	4.61	0.01	2
71	1	5	G	H5''	H	4.09	0.01	2
72	1	5	G	H8	H	7.46	0.01	1
73	1	5	G	C1'	C	92.85	0.01	1
74	1	5	G	C2'	C	75.62	0.01	1
75	1	5	G	C3'	C	72.43	0.01	1
76	1	5	G	C4'	C	82.18	0.01	1
77	1	5	G	C5'	C	64.49	0.01	1
78	1	5	G	C8	C	136.07	0.01	1
79	1	5	G	N1	N	147.02	0.05	1
80	1	5	G	P	P	-1.02	0.01	1
81	1	6	C	H1'	H	5.83	0.01	1
82	1	6	C	H2'	H	4.21	0.01	1
83	1	6	C	H3'	H	4.66	0.01	1
84	1	6	C	H4'	H	4.43	0.01	1
85	1	6	C	H5	H	5.51	0.01	1
86	1	6	C	H5'	H	4.40	0.01	2
87	1	6	C	H5''	H	4.01	0.01	2
88	1	6	C	H6	H	7.47	0.01	1
89	1	6	C	H41	H	8.46	0.01	1
90	1	6	C	H42	H	6.79	0.01	1
91	1	6	C	C1'	C	89.39	0.01	1
92	1	6	C	C2'	C	75.73	0.01	1
93	1	6	C	C3'	C	80.15	0.01	1
94	1	6	C	C4'	C	85.16	0.01	1
95	1	6	C	C5	C	99.45	0.01	1
96	1	6	C	C5'	C	67.15	0.01	1
97	1	6	C	C6	C	141.70	0.01	1
98	1	6	C	N4	N	98.86	0.05	1
99	1	6	C	P	P	-1.39	0.01	1
100	1	7	U	H1'	H	6.12	0.01	1
101	1	7	U	H2'	H	4.50	0.01	1
102	1	7	U	H3'	H	4.57	0.01	1
103	1	7	U	H4'	H	4.36	0.01	1
104	1	7	U	H5	H	6.01	0.01	1
105	1	7	U	H5'	H	4.20	0.01	2
106	1	7	U	H5''	H	4.09	0.01	2
107	1	7	U	H6	H	8.09	0.01	1
108	1	7	U	C1'	C	89.32	0.01	1
109	1	7	U	C2'	C	76.37	0.01	1
110	1	7	U	C3'	C	79.90	0.01	1
111	1	7	U	C4'	C	86.89	0.01	1
112	1	7	U	C5	C	105.48	0.01	1
113	1	7	U	C5'	C	67.90	0.01	1
114	1	7	U	C6	C	144.33	0.01	1
115	1	7	U	P	P	-0.68	0.01	1
116	1	8	U	H1'	H	4.97	0.01	1
117	1	8	U	H2'	H	3.97	0.01	1
118	1	8	U	H3'	H	4.45	0.01	1
119	1	8	U	H4'	H	4.31	0.01	1
120	1	8	U	H5	H	5.33	0.01	1
121	1	8	U	H5'	H	4.08	0.01	2
122	1	8	U	H5''	H	3.89	0.01	2
123	1	8	U	H6	H	7.74	0.01	1
124	1	8	U	C1'	C	89.44	0.01	1
125	1	8	U	C2'	C	77.75	0.01	1
126	1	8	U	C3'	C	80.54	0.01	1
127	1	8	U	C4'	C	85.32	0.01	1
128	1	8	U	C5	C	104.32	0.01	1
129	1	8	U	C5'	C	68.40	0.01	1
130	1	8	U	C6	C	144.20	0.01	1
131	1	8	U	P	P	-1.85	0.01	1
132	1	9	G	H1	H	13.16	0.01	1
133	1	9	G	H1'	H	5.64	0.01	1
134	1	9	G	H2'	H	4.97	0.01	1
135	1	9	G	H3'	H	4.83	0.01	1
136	1	9	G	H4'	H	4.46	0.01	1
137	1	9	G	H5'	H	4.04	0.01	2
138	1	9	G	H5''	H	3.98	0.01	2
139	1	9	G	H8	H	8.01	0.01	1
140	1	9	G	C1'	C	86.80	0.01	1
141	1	9	G	C2'	C	74.30	0.01	1
142	1	9	G	C3'	C	77.64	0.01	1
143	1	9	G	C4'	C	85.40	0.01	1
144	1	9	G	C5'	C	69.80	0.01	1
145	1	9	G	C8	C	137.60	0.01	1
146	1	9	G	N1	N	147.97	0.05	1
147	1	9	G	P	P	-0.67	0.01	1
148	1	10	C	H1'	H	5.77	0.01	1
149	1	10	C	H2'	H	4.60	0.01	1
150	1	10	C	H3'	H	4.31	0.01	1
151	1	10	C	H4'	H	4.64	0.01	1
152	1	10	C	H5	H	5.38	0.01	1
153	1	10	C	H5'	H	4.34	0.01	2
154	1	10	C	H5''	H	4.61	0.01	2
155	1	10	C	H6	H	7.60	0.01	1
156	1	10	C	H41	H	8.49	0.05	1
157	1	10	C	H42	H	6.63	0.05	1
158	1	10	C	C1'	C	94.38	0.01	1
159	1	10	C	C2'	C	74.94	0.01	1
160	1	10	C	C3'	C	74.66	0.01	1
161	1	10	C	C4'	C	83.81	0.01	1
162	1	10	C	C5	C	97.82	0.01	1
163	1	10	C	C5'	C	69.96	0.01	1
164	1	10	C	C6	C	142.48	0.01	1
165	1	10	C	N4	N	96.60	0.01	1
166	1	10	C	P	P	1.47	0.01	1
167	1	11	U	H1'	H	5.67	0.01	1
168	1	11	U	H2'	H	4.66	0.01	1
169	1	11	U	H3	H	13.67	0.01	1
170	1	11	U	H3'	H	4.64	0.01	1
171	1	11	U	H4'	H	4.51	0.01	1
172	1	11	U	H5	H	5.47	0.01	1
173	1	11	U	H5'	H	4.59	0.01	2
174	1	11	U	H5''	H	4.22	0.01	2
175	1	11	U	H6	H	7.95	0.01	1
176	1	11	U	C1'	C	93.52	0.01	1
177	1	11	U	C2'	C	75.34	0.01	1
178	1	11	U	C3'	C	72.80	0.01	1
179	1	11	U	C4'	C	82.03	0.01	1
180	1	11	U	C5	C	103.73	0.01	1
181	1	11	U	C5'	C	65.23	0.01	1
182	1	11	U	C6	C	141.94	0.01	1
183	1	11	U	N3	N	161.90	0.05	1
184	1	11	U	P	P	-0.91	0.01	1
185	1	12	G	H1	H	12.61	0.01	1
186	1	12	G	H1'	H	5.80	0.01	1
187	1	12	G	H2'	H	4.50	0.01	1
188	1	12	G	H3'	H	4.61	0.01	1
189	1	12	G	H4'	H	4.64	0.01	1
190	1	12	G	H5'	H	4.55	0.01	2
191	1	12	G	H5''	H	4.17	0.01	2
192	1	12	G	H8	H	7.77	0.01	1
193	1	12	G	C1'	C	92.86	0.01	1
194	1	12	G	C2'	C	75.38	0.01	1
195	1	12	G	C3'	C	72.88	0.01	1
196	1	12	G	C4'	C	82.11	0.01	1
197	1	12	G	C5'	C	65.52	0.01	1
198	1	12	G	C8	C	136.22	0.01	1
199	1	12	G	N1	N	147.92	0.05	1
200	1	12	G	P	P	-0.74	0.01	1
201	1	13	C	H1'	H	5.47	0.01	1
202	1	13	C	H2'	H	4.16	0.01	1
203	1	13	C	H3'	H	4.44	0.01	1
204	1	13	C	H4'	H	4.37	0.01	1
205	1	13	C	H5	H	5.26	0.01	1
206	1	13	C	H5'	H	4.55	0.01	2
207	1	13	C	H5''	H	4.05	0.01	2
208	1	13	C	H6	H	7.65	0.01	1
209	1	13	C	H41	H	8.23	0.01	1
210	1	13	C	H42	H	6.78	0.01	1
211	1	13	C	C1'	C	94.39	0.01	1
212	1	13	C	C2'	C	75.70	0.01	1
213	1	13	C	C3'	C	72.16	0.01	1
214	1	13	C	C4'	C	82.18	0.01	1
215	1	13	C	C5	C	96.98	0.01	1
216	1	13	C	C5'	C	64.46	0.01	1
217	1	13	C	C6	C	141.13	0.01	1
218	1	13	C	N4	N	100.42	0.01	1
219	1	13	C	P	P	-1.19	0.01	1
220	1	14	C	H1'	H	6.10	0.01	1
221	1	14	C	H2'	H	4.63	0.01	1
222	1	14	C	H3'	H	4.94	0.01	1
223	1	14	C	H4'	H	4.41	0.01	1
224	1	14	C	H5	H	5.54	0.01	1
225	1	14	C	H5'	H	4.50	0.01	2
226	1	14	C	H5''	H	4.09	0.01	2
227	1	14	C	H6	H	7.48	0.01	1
228	1	14	C	H41	H	8.49	0.01	1
229	1	14	C	H42	H	7.00	0.01	1
230	1	14	C	C1'	C	92.02	0.01	1
231	1	14	C	C2'	C	85.19	0.01	1
232	1	14	C	C3'	C	77.89	0.01	1
233	1	14	C	C4'	C	85.56	0.01	1
234	1	14	C	C5	C	99.16	0.01	1
235	1	14	C	C5'	C	65.73	0.01	1
236	1	14	C	C6	C	141.70	0.01	1
237	1	14	C	N4	N	98.99	0.02	1
238	1	14	C	P	P	-1.02	0.01	1

Release date

2023-03-13

Citation

Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop
Oxenfarth, A., Kuemmerer, F., Bottaro, S., Schnieders, R., Pinter, G., Jonker, H.R.A., Fuertig, B., Richter, C., Blackledge, M., Lindorff-Larsen, K., Schwalbe, H.
J. Am. Chem. Soc. (2023), 145, 16557-16572, PubMed 37479220 , DOI 10.1021/jacs.3c03578 , Abstract

Related entities 1. RNA hairpin with CUUG tetraloop, : 1 : 8 entities Detail

Experiments performed 18 experiments Detail