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BMRB: 17292

2L5Z

NMR structure of the A730 loop of the Neurospora VS ribozyme

Authors

Desjardins, G., Bonneau, E., Girard, N., Boisbouvier, J., Legault, P.

Assembly

26-MER

Entity

1. 26-MER (polymer, Thiol state: not present), 26 monomers, 8484.076 Da Detail

GAGCUGCAGC ACGAAAGUGA CGGCUC

Formula weight

8484.076 Da

Source organism

Neurospora

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	99.0 % (406 of 410)	98.7 % (222 of 225)	100.0 % (173 of 173)	91.7 % (11 of 12)
Suger, PO4	100.0 % (286 of 286)	100.0 % (156 of 156)	100.0 % (130 of 130)
Nucleobase	96.8 % (120 of 124)	95.7 % (66 of 69)	100.0 % (43 of 43)	91.7 % (11 of 12)
Aromatic	98.2 % (108 of 110)	98.2 % (54 of 55)	100.0 % (43 of 43)	91.7 % (11 of 12)

1. VS ribozyme SVI RNA (26-MER)

GAGCUGCAGC ACGAAAGUGA CGGCUC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
1	VS ribozyme SVI RNA (26-MER)	natural abundance	0.4 ~ 1.8 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium cacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
8	VS ribozyme SVI RNA (26-MER)	natural abundance	0.4 ~ 1.8 (±0.1) mM
9	D2O	natural abundance	100 %
10	sodium cacodylate	natural abundance	10 mM
11	KCl	natural abundance	50 mM
12	NaN3	natural abundance	0.05 mM
13	MgCl2	natural abundance	5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
14	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %
17	sodium cacodylate	natural abundance	10 mM
18	KCl	natural abundance	50 mM
19	NaN3	natural abundance	0.05 mM
20	MgCl2	natural abundance	5 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
21	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
22	D2O	natural abundance	100 %
23	sodium cacodylate	natural abundance	10 mM
24	KCl	natural abundance	50 mM
25	NaN3	natural abundance	0.05 mM
26	MgCl2	natural abundance	5 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
27	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %
30	sodium cacodylate	natural abundance	10 mM
31	KCl	natural abundance	50 mM
32	NaN3	natural abundance	0.05 mM
33	MgCl2	natural abundance	5 mM

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2 ~17 mg/mL Pf1 filamentous phage solution (ASLA biotech.)

#	Name	Isotope labeling	Concentration
40	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 (±0.1) mM
41	H2O	natural abundance	90 %
42	D2O	natural abundance	10 %
43	sodium cacodylate	natural abundance	10 mM
44	KCl	natural abundance	50 mM
45	NaN3	natural abundance	0.05 mM
46	MgCl2	natural abundance	5 mM
47	Pf1 filamentous phage	natural abundance	17 mg/mL

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2 ~17 mg/mL Pf1 filamentous phage solution (ASLA biotech.)

#	Name	Isotope labeling	Concentration
48	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 (±0.1) mM
49	D2O	natural abundance	100 %
50	sodium cacodylate	natural abundance	10 mM
51	KCl	natural abundance	50 mM
52	NaN3	natural abundance	0.05 mM
53	MgCl2	natural abundance	5 mM
54	Pf1 filamentous phage	natural abundance	17 mg/mL

Release date

2011-01-26

Citation

NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site
Desjardins, G., Bonneau, E., Girard, N., Boisbouvier, J., Legault, P.
Nucleic Acids Res. (2011), 39, 4427-4437, PubMed 21266483 , DOI 10.1093/nar/gkq1244 , Abstract

Related entities 1. 26-MER, : 1 : 1 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

2 2D 1H-13C HMQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

3 2D 1H-15N MQ-(HC)N(C)H

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

4 3D CT-HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

6 3D 13C-edited HMQC-NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

7 1D flip-back watergate 1H

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
1	VS ribozyme SVI RNA (26-MER)	natural abundance	0.4 ~ 1.8 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium cacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

8 2D flip-back watergate NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
1	VS ribozyme SVI RNA (26-MER)	natural abundance	0.4 ~ 1.8 (±0.1) mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium cacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

9 2D imino- and amino-optimized 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
14	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %
17	sodium cacodylate	natural abundance	10 mM
18	KCl	natural abundance	50 mM
19	NaN3	natural abundance	0.05 mM
20	MgCl2	natural abundance	5 mM

10 2D H(NCCC)H for uracil and cytosine residues

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
27	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %
30	sodium cacodylate	natural abundance	10 mM
31	KCl	natural abundance	50 mM
32	NaN3	natural abundance	0.05 mM
33	MgCl2	natural abundance	5 mM

11 2D H(NC)-TOCSY-(C)H for guanosine residues

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
27	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %
30	sodium cacodylate	natural abundance	10 mM
31	KCl	natural abundance	50 mM
32	NaN3	natural abundance	0.05 mM
33	MgCl2	natural abundance	5 mM

12 2D (H)N(C)-TOCSY-(C)H for adenosine residues

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
27	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %
30	sodium cacodylate	natural abundance	10 mM
31	KCl	natural abundance	50 mM
32	NaN3	natural abundance	0.05 mM
33	MgCl2	natural abundance	5 mM

13 2D 1H-15N CPMG-NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
14	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %
17	sodium cacodylate	natural abundance	10 mM
18	KCl	natural abundance	50 mM
19	NaN3	natural abundance	0.05 mM
20	MgCl2	natural abundance	5 mM

14 2D 1H 15N HMQC optimized for transfers via J=7.0 Hz and J=21 Hz

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
21	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
22	D2O	natural abundance	100 %
23	sodium cacodylate	natural abundance	10 mM
24	KCl	natural abundance	50 mM
25	NaN3	natural abundance	0.05 mM
26	MgCl2	natural abundance	5 mM

15 2D HNN-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
14	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 ~ 1.8 (±0.1) mM
15	H2O	natural abundance	90 %
16	D2O	natural abundance	10 %
17	sodium cacodylate	natural abundance	10 mM
18	KCl	natural abundance	50 mM
19	NaN3	natural abundance	0.05 mM
20	MgCl2	natural abundance	5 mM

16 2D DQF COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
8	VS ribozyme SVI RNA (26-MER)	natural abundance	0.4 ~ 1.8 (±0.1) mM
9	D2O	natural abundance	100 %
10	sodium cacodylate	natural abundance	10 mM
11	KCl	natural abundance	50 mM
12	NaN3	natural abundance	0.05 mM
13	MgCl2	natural abundance	5 mM

17 3D HCCH-E.COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

18 2D imino-optimized 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2 ~17 mg/mL Pf1 filamentous phage solution (ASLA biotech.)

#	Name	Isotope labeling	Concentration
40	VS ribozyme SVI RNA (26-MER)	[U-15N]	0.4 (±0.1) mM
41	H2O	natural abundance	90 %
42	D2O	natural abundance	10 %
43	sodium cacodylate	natural abundance	10 mM
44	KCl	natural abundance	50 mM
45	NaN3	natural abundance	0.05 mM
46	MgCl2	natural abundance	5 mM
47	Pf1 filamentous phage	natural abundance	17 mg/mL

19 Spin-state selective experiments

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2 ~17 mg/mL Pf1 filamentous phage solution (ASLA biotech.)

#	Name	Isotope labeling	Concentration
48	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 (±0.1) mM
49	D2O	natural abundance	100 %
50	sodium cacodylate	natural abundance	10 mM
51	KCl	natural abundance	50 mM
52	NaN3	natural abundance	0.05 mM
53	MgCl2	natural abundance	5 mM
54	Pf1 filamentous phage	natural abundance	17 mg/mL

20 Spin-state selective experiments

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 10 mM sodium cacodylate, pH 6.5, 50 mM KCl, 0.05 mM NaN3 and 5 mM MgCl2

#	Name	Isotope labeling	Concentration
34	VS ribozyme SVI RNA (26-MER)	[U-13C; U-15N]	0.4 ~ 1.8 (±0.1) mM
35	D2O	natural abundance	100 %
36	sodium cacodylate	natural abundance	10 mM
37	KCl	natural abundance	50 mM
38	NaN3	natural abundance	0.05 mM
39	MgCl2	natural abundance	5 mM

nullKeywords internal loop, RNA, VS ribozyme

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Found 1 Document (0.589 seconds)

BMRB: 17292

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Related entities 1. 26-MER, : 1 : 1 entities Detail

Experiments performed 20 experiments Detail

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