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BMRB: 18656

2LX1

Major Conformation of the Internal Loop 5'GAGU/3'UGAG

Authors

Kennedy, S.D., Turner, D.H.

Assembly

Internal Loop 5'GAGU/3'UGAG

Entity

1. Internal Loop 5'GAGU/3'UGAG (polymer, Thiol state: not present), 11 monomers, 3609.150 × 2 Da Detail

GACGAGUGUC A

Total weight

7218.3 Da

Max. entity weight

3609.15 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 62.5 %, Completeness (bb): 57.6 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	62.5 % (115 of 184)	97.9 % (92 of 94)	17.8 % (13 of 73)	0.0 % (0 of 6)	90.9 % (10 of 11)
Suger, PO4	57.6 % (76 of 132)	100.0 % (66 of 66)	0.0 % (0 of 55)		90.9 % (10 of 11)
Nucleobase	75.0 % (39 of 52)	92.9 % (26 of 28)	72.2 % (13 of 18)	0.0 % (0 of 6)
Aromatic	72.9 % (35 of 48)	91.7 % (22 of 24)	72.2 % (13 of 18)	0.0 % (0 of 6)

1. RNA loop

GACGAGUGUC A

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
7	RNA_loop	natural abundance	1.5 mM
8	sodium chloride	natural abundance	80 mM
9	sodium phosphate	natural abundance	10 mM
10	EDTA	natural abundance	0.05 mM
11	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 47.8 %, Completeness (bb): 39.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	47.8 % (176 of 368)	78.7 % (148 of 188)	8.9 % (13 of 146)	41.7 % (5 of 12)	45.5 % (10 of 22)
Suger, PO4	39.8 % (105 of 264)	72.0 % (95 of 132)	0.0 % (0 of 110)		45.5 % (10 of 22)
Nucleobase	68.3 % (71 of 104)	94.6 % (53 of 56)	36.1 % (13 of 36)	41.7 % (5 of 12)
Aromatic	65.6 % (63 of 96)	93.8 % (45 of 48)	36.1 % (13 of 36)	41.7 % (5 of 12)

1. RNA loop

GACGAGUGUC A

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
7	RNA_loop	natural abundance	1.5 mM
8	sodium chloride	natural abundance	80 mM
9	sodium phosphate	natural abundance	10 mM
10	EDTA	natural abundance	0.05 mM
11	D2O	natural abundance	100 %

Release date

2011-05-04

Citation

Novel conformation of an RNA structural switch
Kennedy, S.D., Kierzek, R., Turner, D.H.
Biochemistry (2012), 51, 9257-9259, PubMed 23134175 , DOI 10.1021/bi301372t , Abstract

Related entities 1. Internal Loop 5'GAGU/3'UGAG, : 1 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 2D 1H-1H TOCSY 30 ms

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

4 2D 1H-1H NOESY 75 ms

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 2D 1H-1H NOESY 150 ms

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 274 K, pH 6.1

#	Name	Isotope labeling	Concentration
1	RNA_loop	natural abundance	1.5 mM
2	sodium chloride	natural abundance	80 mM
3	sodium phosphate	natural abundance	10 mM
4	EDTA	natural abundance	0.05 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

6 2D 1H-13C HSQC