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BMRB: 34670

NMR Structure of the U3 RNA G-quadruplex

Authors

Assembly

RNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3')

Entity

1. RNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3'), entity 1 (polymer, Thiol state: not present), 23 monomers, 7648.531 Da Detail

CAGGGAGGUG UGGCCUGGGC GGG

2. RNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3'), entity K (non-polymer), 39.098 × 2 Da

Total weight

7726.7266 Da

Max. entity weight

7648.531 Da

Source organism

HIV-1 06TG.HT008

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chemcal Shifts

¹H: 177, ¹³C: 134, ¹⁵N: 12 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err
1	1	1	C	H1'	H	5.505	0.003
2	1	1	C	H2'	H	3.909	0.004
3	1	1	C	H3'	H	4.215	0.003
4	1	1	C	H4'	H	3.968	0.004
5	1	1	C	H5	H	5.620	0.006
6	1	1	C	H5'	H	3.562	0.006
7	1	1	C	H5''	H	3.494	0.004
8	1	1	C	H6	H	7.380	0.013
9	1	1	C	C1'	C	89.600	0.000
10	1	1	C	C2'	C	73.122	0.000
11	1	1	C	C3'	C	72.331	0.000
12	1	1	C	C4'	C	83.495	0.000
13	1	1	C	C5	C	95.868	0.000
14	1	1	C	C5'	C	60.698	0.014
15	1	1	C	C6	C	140.382	0.000
16	1	2	A	H1'	H	5.584	0.003
17	1	2	A	H2	H	7.934	0.003
18	1	2	A	H2'	H	4.412	0.002
19	1	2	A	H3'	H	4.704	0.001
20	1	2	A	H4'	H	4.378	0.003
21	1	2	A	H5'	H	3.984	0.004
22	1	2	A	H5''	H	3.909	0.003
23	1	2	A	H8	H	8.038	0.004
24	1	2	A	C1'	C	87.281	0.000
25	1	2	A	C2	C	152.460	0.000
26	1	2	A	C3'	C	73.854	0.000
27	1	2	A	C4'	C	82.397	0.000
28	1	2	A	C5'	C	64.990	0.010
29	1	2	A	C8	C	140.953	0.000
30	1	3	G	H1	H	11.811	0.004
31	1	3	G	H1'	H	5.838	0.003
32	1	3	G	H2'	H	5.001	0.005
33	1	3	G	H3'	H	4.933	0.003
34	1	3	G	H4'	H	4.585	0.004
35	1	3	G	H5'	H	4.255	0.002
36	1	3	G	H5''	H	4.205	0.002
37	1	3	G	H8	H	8.075	0.002
38	1	3	G	C1'	C	84.608	0.000
39	1	3	G	C2'	C	72.182	0.000
40	1	3	G	C4'	C	80.081	0.000
41	1	3	G	C5	C	115.335	0.004
42	1	3	G	C8	C	135.079	0.000
43	1	3	G	N1	N	144.238	0.000
44	1	4	G	H1	H	11.175	0.003
45	1	4	G	H1'	H	5.892	0.003
46	1	4	G	H2'	H	4.852	0.001
47	1	4	G	H3'	H	4.730	0.002
48	1	4	G	H8	H	7.916	0.003
49	1	4	G	H21	H	9.222	0.005
50	1	4	G	C1'	C	87.942	0.000
51	1	4	G	C2'	C	72.108	0.000
52	1	4	G	C3'	C	73.474	0.000
53	1	4	G	C5	C	114.594	0.005
54	1	4	G	C8	C	135.514	0.000
55	1	4	G	N1	N	142.195	0.000
56	1	5	G	H1	H	11.143	0.003
57	1	5	G	H1'	H	6.128	0.006
58	1	5	G	H2'	H	4.778	0.000
59	1	5	G	H3'	H	5.069	0.003
60	1	5	G	H4'	H	4.292	0.001
61	1	5	G	H5'	H	4.736	0.002
62	1	5	G	H5''	H	4.697	0.003
63	1	5	G	H8	H	7.676	0.002
64	1	5	G	C1'	C	85.589	0.000
65	1	5	G	C2'	C	74.292	0.000
66	1	5	G	C3'	C	77.745	0.000
67	1	5	G	C4'	C	83.428	0.000
68	1	5	G	C5	C	113.511	0.000
69	1	5	G	C8	C	136.347	0.000
70	1	5	G	N1	N	144.629	0.000
71	1	6	A	H1'	H	6.342	0.003
72	1	6	A	H2	H	8.368	0.002
73	1	6	A	H2'	H	4.997	0.004
74	1	6	A	H3'	H	5.086	0.004
75	1	6	A	H4'	H	4.845	0.003
76	1	6	A	H5'	H	4.523	0.004
77	1	6	A	H5''	H	4.399	0.002
78	1	6	A	H8	H	8.622	0.001
79	1	6	A	C1'	C	85.796	0.000
80	1	6	A	C2	C	153.262	0.000
81	1	6	A	C2'	C	74.614	0.000
82	1	6	A	C3'	C	77.319	0.000
83	1	6	A	C4'	C	83.986	0.000
84	1	6	A	C8	C	139.653	0.000
85	1	7	G	H1	H	11.605	0.004
86	1	7	G	H1'	H	5.726	0.014
87	1	7	G	H2'	H	4.711	0.000
88	1	7	G	H3'	H	4.896	0.007
89	1	7	G	H4'	H	4.563	0.003
90	1	7	G	H5'	H	4.393	0.000
91	1	7	G	H5''	H	4.245	0.000
92	1	7	G	H8	H	7.864	0.001
93	1	7	G	C1'	C	87.788	0.000
94	1	7	G	C2'	C	72.803	0.000
95	1	7	G	C5	C	116.358	0.005
96	1	7	G	C8	C	135.165	0.000
97	1	7	G	N1	N	144.463	0.000
98	1	8	G	H1	H	11.528	0.004
99	1	8	G	H1'	H	5.948	0.003
100	1	8	G	H2'	H	4.871	0.003
101	1	8	G	H3'	H	4.959	0.002
102	1	8	G	H4'	H	4.648	0.001
103	1	8	G	H5'	H	4.252	0.001
104	1	8	G	H5''	H	4.229	0.000
105	1	8	G	H8	H	8.026	0.003
106	1	8	G	C1'	C	85.739	0.000
107	1	8	G	C2'	C	76.710	0.000
108	1	8	G	C3'	C	75.089	0.000
109	1	8	G	C4'	C	81.679	0.000
110	1	8	G	C5	C	114.403	0.010
111	1	8	G	C8	C	135.775	0.000
112	1	8	G	N1	N	143.456	0.000
113	1	9	U	H1'	H	6.086	0.004
114	1	9	U	H2'	H	4.571	0.003
115	1	9	U	H3'	H	4.732	0.003
116	1	9	U	H4'	H	4.498	0.004
117	1	9	U	H5	H	5.982	0.005
118	1	9	U	H5'	H	4.270	0.002
119	1	9	U	H5''	H	4.208	0.001
120	1	9	U	H6	H	7.889	0.000
121	1	9	U	C1'	C	87.251	0.000
122	1	9	U	C2'	C	72.335	0.000
123	1	9	U	C3'	C	74.589	0.000
124	1	9	U	C4'	C	84.029	0.000
125	1	9	U	C5	C	103.048	0.000
126	1	9	U	C6	C	141.930	0.000
127	1	10	G	H1'	H	5.578	0.003
128	1	10	G	H2'	H	4.059	0.003
129	1	10	G	H3'	H	4.533	0.003
130	1	10	G	H4'	H	3.583	0.005
131	1	10	G	H5'	H	4.235	0.004
132	1	10	G	H5''	H	3.986	0.003
133	1	10	G	H8	H	7.847	0.004
134	1	10	G	C1'	C	84.916	0.000
135	1	10	G	C2'	C	76.551	0.000
136	1	10	G	C3'	C	76.583	0.000
137	1	10	G	C4'	C	83.716	0.000
138	1	10	G	C5	C	113.907	0.000
139	1	10	G	C5'	C	65.932	0.010
140	1	10	G	C8	C	136.228	0.000
141	1	11	U	H1'	H	5.626	0.002
142	1	11	U	H2'	H	3.935	0.004
143	1	11	U	H3'	H	4.435	0.003
144	1	11	U	H4'	H	4.212	0.004
145	1	11	U	H5	H	5.606	0.003
146	1	11	U	H5'	H	3.487	0.006
147	1	11	U	H5''	H	2.756	0.003
148	1	11	U	H6	H	7.412	0.011
149	1	11	U	C1'	C	87.211	0.000
150	1	11	U	C2'	C	75.460	0.000
151	1	11	U	C3'	C	75.726	0.000
152	1	11	U	C4'	C	83.197	0.000
153	1	11	U	C5	C	101.328	0.000
154	1	11	U	C5'	C	64.538	0.002
155	1	11	U	C6	C	141.257	0.000
156	1	12	G	H1	H	11.338	0.003
157	1	12	G	H1'	H	5.947	0.006
158	1	12	G	H2'	H	4.957	0.002
159	1	12	G	H3'	H	4.731	0.000
160	1	12	G	H4'	H	4.387	0.000
161	1	12	G	H5'	H	4.213	0.000
162	1	12	G	H5''	H	4.230	0.000
163	1	12	G	H8	H	8.037	0.003
164	1	12	G	C1'	C	87.892	0.000
165	1	12	G	C2'	C	74.847	0.000
166	1	12	G	C5	C	116.182	0.000
167	1	12	G	C8	C	138.678	0.000
168	1	12	G	N1	N	144.228	0.000
169	1	13	G	H1'	H	6.052	0.003
170	1	13	G	H2'	H	5.018	0.003
171	1	13	G	H3'	H	4.918	0.004
172	1	13	G	H4'	H	4.738	0.003
173	1	13	G	H5'	H	4.472	0.005
174	1	13	G	H5''	H	4.382	0.003
175	1	13	G	H8	H	8.216	0.003
176	1	13	G	C1'	C	88.191	0.000
177	1	13	G	C2'	C	72.732	0.000
178	1	13	G	C3'	C	74.311	0.000
179	1	13	G	C4'	C	82.461	0.000
180	1	13	G	C5	C	116.778	0.000
181	1	13	G	C8	C	137.850	0.000
182	1	14	C	H1'	H	6.035	0.003
183	1	14	C	H2'	H	4.448	0.001
184	1	14	C	H3'	H	4.730	0.004
185	1	14	C	H4'	H	4.537	0.011
186	1	14	C	H5	H	5.936	0.005
187	1	14	C	H5'	H	4.298	0.001
188	1	14	C	H5''	H	4.472	0.002
189	1	14	C	H6	H	7.903	0.001
190	1	14	C	C1'	C	89.431	0.000
191	1	14	C	C2'	C	75.726	0.000
192	1	14	C	C3'	C	73.640	0.000
193	1	14	C	C4'	C	84.966	0.000
194	1	14	C	C5	C	96.275	0.000
195	1	14	C	C6	C	141.198	0.000
196	1	15	C	H1'	H	6.083	0.004
197	1	15	C	H2'	H	4.418	0.001
198	1	15	C	H3'	H	4.652	0.005
199	1	15	C	H4'	H	4.557	0.005
200	1	15	C	H5	H	6.126	0.005
201	1	15	C	H5'	H	4.379	0.003
202	1	15	C	H5''	H	4.226	0.000
203	1	15	C	H6	H	7.916	0.001
204	1	15	C	C1'	C	88.188	0.000
205	1	15	C	C2'	C	73.742	0.000
206	1	15	C	C3'	C	74.407	0.000
207	1	15	C	C4'	C	83.896	0.000
208	1	15	C	C5	C	96.908	0.000
209	1	15	C	C5'	C	67.129	0.015
210	1	15	C	C6	C	141.306	0.000
211	1	16	U	H1'	H	5.784	0.003
212	1	16	U	H2'	H	4.209	0.005
213	1	16	U	H3'	H	4.711	0.002
214	1	16	U	H4'	H	4.366	0.004
215	1	16	U	H5	H	5.730	0.003
216	1	16	U	H5'	H	4.170	0.004
217	1	16	U	H5''	H	4.123	0.001
218	1	16	U	H6	H	7.711	0.004
219	1	16	U	C1'	C	88.164	0.000
220	1	16	U	C2'	C	73.804	0.000
221	1	16	U	C3'	C	74.867	0.000
222	1	16	U	C4'	C	82.255	0.000
223	1	16	U	C5	C	102.729	0.000
224	1	16	U	C6	C	141.279	0.000
225	1	17	G	H1	H	11.971	0.003
226	1	17	G	H1'	H	5.872	0.008
227	1	17	G	H2'	H	5.013	0.003
228	1	17	G	H3'	H	4.962	0.003
229	1	17	G	H4'	H	4.590	0.003
230	1	17	G	H5'	H	4.210	0.002
231	1	17	G	H5''	H	4.170	0.002
232	1	17	G	H8	H	8.194	0.002
233	1	17	G	C1'	C	83.051	0.000
234	1	17	G	C2'	C	71.346	0.000
235	1	17	G	C3'	C	74.702	0.000
236	1	17	G	C4'	C	82.621	0.000
237	1	17	G	C5	C	115.486	0.011
238	1	17	G	C8	C	136.160	0.000
239	1	17	G	N1	N	144.554	0.000
240	1	18	G	H1	H	11.361	0.006
241	1	18	G	H1'	H	5.930	0.004
242	1	18	G	H2'	H	4.849	0.005
243	1	18	G	H3'	H	4.750	0.001
244	1	18	G	H4'	H	4.731	0.002
245	1	18	G	H5'	H	4.592	0.005
246	1	18	G	H5''	H	4.571	0.001
247	1	18	G	H8	H	7.988	0.004
248	1	18	G	C1'	C	87.561	0.000
249	1	18	G	C2'	C	71.950	0.000
250	1	18	G	C3'	C	73.707	0.000
251	1	18	G	C4'	C	81.934	0.000
252	1	18	G	C5	C	114.911	0.005
253	1	18	G	C5'	C	67.058	0.009
254	1	18	G	C8	C	136.000	0.000
255	1	18	G	N1	N	142.788	0.000
256	1	19	G	H1	H	11.354	0.004
257	1	19	G	H1'	H	6.201	0.006
258	1	19	G	H2'	H	4.730	0.001
259	1	19	G	H3'	H	4.963	0.004
260	1	19	G	H4'	H	4.416	0.004
261	1	19	G	H5'	H	4.768	0.002
262	1	19	G	H5''	H	4.745	0.004
263	1	19	G	H8	H	7.985	0.002
264	1	19	G	C1'	C	84.585	0.000
265	1	19	G	C2'	C	75.554	0.000
266	1	19	G	C4'	C	82.412	0.000
267	1	19	G	C5	C	114.299	0.005
268	1	19	G	C8	C	136.645	0.000
269	1	19	G	N1	N	143.977	0.000
270	1	20	C	H1'	H	6.355	0.002
271	1	20	C	H2'	H	4.547	0.002
272	1	20	C	H3'	H	4.970	0.004
273	1	20	C	H4'	H	4.769	0.003
274	1	20	C	H5	H	6.267	0.003
275	1	20	C	H5'	H	4.414	0.001
276	1	20	C	H6	H	8.005	0.003
277	1	20	C	C1'	C	87.104	0.000
278	1	20	C	C2'	C	73.849	0.000
279	1	20	C	C3'	C	76.974	0.000
280	1	20	C	C4'	C	83.054	0.000
281	1	20	C	C5	C	97.506	0.000
282	1	20	C	C6	C	141.154	0.000
283	1	21	G	H1	H	11.102	0.004
284	1	21	G	H1'	H	5.797	0.003
285	1	21	G	H2'	H	4.809	0.001
286	1	21	G	H3'	H	4.898	0.002
287	1	21	G	H4'	H	4.708	0.004
288	1	21	G	H8	H	7.910	0.003
289	1	21	G	C1'	C	91.562	0.000
290	1	21	G	C2'	C	75.085	0.000
291	1	21	G	C3'	C	71.100	0.000
292	1	21	G	C4'	C	81.889	0.000
293	1	21	G	C5	C	116.428	0.007
294	1	21	G	C8	C	134.821	0.000
295	1	21	G	N1	N	144.075	0.000
296	1	22	G	H1	H	11.465	0.004
297	1	22	G	H1'	H	5.856	0.005
298	1	22	G	H2'	H	4.858	0.003
299	1	22	G	H3'	H	4.893	0.003
300	1	22	G	H4'	H	4.567	0.003
301	1	22	G	H5'	H	4.393	0.000
302	1	22	G	H5''	H	4.246	0.001
303	1	22	G	H8	H	7.862	0.004
304	1	22	G	C1'	C	87.022	0.000
305	1	22	G	C2'	C	73.504	0.000
306	1	22	G	C4'	C	79.667	0.000
307	1	22	G	C5	C	114.784	0.013
308	1	22	G	C8	C	134.647	0.000
309	1	22	G	N1	N	143.489	0.000
310	1	23	G	H1	H	11.493	0.004
311	1	23	G	H1'	H	6.090	0.004
312	1	23	G	H2'	H	4.446	0.005
313	1	23	G	H3'	H	4.514	0.004
314	1	23	G	H4'	H	4.318	0.002
315	1	23	G	H5'	H	4.565	0.004
316	1	23	G	H5''	H	4.499	0.004
317	1	23	G	H8	H	8.158	0.002
318	1	23	G	C1'	C	88.875	0.000
319	1	23	G	C2'	C	73.492	0.000
320	1	23	G	C3'	C	69.736	0.000
321	1	23	G	C5	C	115.123	0.004
322	1	23	G	C8	C	136.490	0.000
323	1	23	G	N1	N	144.437	0.000

Release date

2021-10-24

Citation

HIV-1 genomic RNA U3 region forms a stable quadruplex-hairpin structure
Marquevielle, J., Amrane, S.
Biophys. Chem. (2021), 272, 106567-106567, PubMed 33713997 , DOI 10.1016/j.bpc.2021.106567 , Abstract

Experiments performed 4 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	rHIVpro3	1H		1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	rHIVpro3	1H		1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	rHIVpro3	1H		1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	rHIVpro3	1H		1.5 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34670_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34670_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	323		100.0 (chain: 1, length: 23)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 23, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 177
- ¹³C chemical shifts: 134
- ¹⁵N chemical shifts: 12

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	G	C5	115.335
4	G	H21	9.222
4	G	C5	114.594
5	G	C5	113.511
7	G	C5	116.358
8	G	C5	114.403
10	G	C5	113.907
12	G	C5	116.182
13	G	C5	116.778
17	G	C5	115.486
18	G	C5	114.911
19	G	C5	114.299
21	G	C5	116.428
22	G	C5	114.784
23	G	C5	115.123

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	195	176	90.3
¹³C chemical shifts	147	120	81.6
¹⁵N chemical shifts	17	12	70.6

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	138	132	95.7
¹³C chemical shifts	115	88	76.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	44	77.2
¹³C chemical shifts	32	32	100.0
¹⁵N chemical shifts	17	12	70.6

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	18	100.0

Histogram of normalized assigned chemical shifts

Keywords HIV-1, VIRUS

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BMRB: 34670

Experiments performed 4 experiments Detail

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Chemical shift validation 4 contents Detail