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BMRB: 25655

2N3R

NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

Authors

Bonneau, E., Girard, N., Lemieux, S., Legault, P.

Assembly

II-III-VI three-way junction from the VS ribozyme in complex with MAGNESIUM

Entity

1. RNA (62-MER) (polymer, Thiol state: not present), 62 monomers, 20084.95 Da Detail

GCAGCAGGGA ACUCACGCUU GCGUAGAGGC UAAGUGCUUC GGCACAGCAC AAGCCCGCUG CG

2. MAGNESIUM ION (non-polymer), 24.305 × 8 Da
3. WATER (water), 18.015 × 13 Da

Total weight

20279.389 Da

Max. entity weight

20084.95 Da

Source organism

Neurospora crassa

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.4 %, Completeness (bb): 91.9 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	93.4 % (921 of 986)	92.4 % (502 of 543)	95.2 % (394 of 414)	86.2 % (25 of 29)
Suger, PO4	91.9 % (627 of 682)	90.6 % (337 of 372)	93.5 % (290 of 310)
Nucleobase	96.7 % (294 of 304)	96.5 % (165 of 171)	100.0 % (104 of 104)	86.2 % (25 of 29)
Aromatic	97.0 % (258 of 266)	97.0 % (129 of 133)	100.0 % (104 of 104)	86.2 % (25 of 29)

1. RNA (62-MER)

GCAGCAGGGA ACUCACGCUU GCGUAGAGGC UAAGUGCUUC GGCACAGCAC AAGCCCGCUG CG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	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

#	Name	Isotope labeling	Concentration
8	RNA (62-MER)	[U-13C; U-15N]	2 mM
9	D2O	natural abundance	100 %
10	NaCacodylate	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 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
14	RNA (62-MER)	[U-13C; U-15N]-Ade	2 mM
15	D2O	natural abundance	100 %
16	NaCacodylate	natural abundance	10 mM
17	KCl	natural abundance	50 mM
18	NaN3	natural abundance	0.05 mM
19	MgCl2	natural abundance	5 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
20	RNA (62-MER)	[U-13C; U-15N]-Cyt	2 mM
21	D2O	natural abundance	100 %
22	NaCacodylate	natural abundance	10 mM
23	KCl	natural abundance	50 mM
24	NaN3	natural abundance	0.05 mM
25	MgCl2	natural abundance	5 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
26	RNA (62-MER)	[U-13C; U-15N]-Gua	2.5 mM
27	D2O	natural abundance	100 %
28	NaCacodylate	natural abundance	10 mM
29	KCl	natural abundance	50 mM
30	NaN3	natural abundance	0.05 mM
31	MgCl2	natural abundance	5 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
32	RNA (62-MER)	[U-13C; U-15N]	2 mM
33	D2O	natural abundance	10 %
34	H2O	natural abundance	90 %
35	NaCacodylate	natural abundance	10 mM
36	KCl	natural abundance	50 mM
37	NaN3	natural abundance	0.05 mM
38	MgCl2	natural abundance	5 mM

Release date

2015-07-02

Citation

The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure
Bonneau, E., Girard, N., Lemieux, S., Legault, P.
RNA (2015), 21, 1621-1632, PubMed 26124200 , DOI 10.1261/rna.052076.115 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25654 released on 2015-07-02
Title NMR structure of the II-III-VI three-way junction from the VS ribozyme

Experiments performed 31 experiments Detail

1 1D 1H watergate

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

2 2D 1H-15N HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

3 2D 1H-15N HSQC NH2 only

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

4 2D HNN COSY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

5 2D 1H-1H NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

6 2D 1H-15N CPMG-NOESY

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

7 3D 15N-edited NOESY-HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (62-MER)	[U-15N]	2 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCacodylate	natural abundance	10 mM
5	KCl	natural abundance	50 mM
6	NaN3	natural abundance	0.05 mM
7	MgCl2	natural abundance	5 mM

8 3D 15N/13C-edited NOESY-HSQC

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
32	RNA (62-MER)	[U-13C; U-15N]	2 mM
33	D2O	natural abundance	10 %
34	H2O	natural abundance	90 %
35	NaCacodylate	natural abundance	10 mM
36	KCl	natural abundance	50 mM
37	NaN3	natural abundance	0.05 mM
38	MgCl2	natural abundance	5 mM

9 2D G-specific H(NC)-TOCSY-(C)H

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
32	RNA (62-MER)	[U-13C; U-15N]	2 mM
33	D2O	natural abundance	10 %
34	H2O	natural abundance	90 %
35	NaCacodylate	natural abundance	10 mM
36	KCl	natural abundance	50 mM
37	NaN3	natural abundance	0.05 mM
38	MgCl2	natural abundance	5 mM

10 2D A-specific H(NC)-TOCSY-(C)H

Instrument

Varian Unity - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
32	RNA (62-MER)	[U-13C; U-15N]	2 mM
33	D2O	natural abundance	10 %
34	H2O	natural abundance	90 %
35	NaCacodylate	natural abundance	10 mM
36	KCl	natural abundance	50 mM
37	NaN3	natural abundance	0.05 mM
38	MgCl2	natural abundance	5 mM

11 2D 1H-15N MQ-(HC)N(C)H