BMRB: 16950

The Structure of RNA Internal Loops with Tandem AG Pairs: 5'AAGU/3'UGAA

Authors

Hammond, N.B., Kennedy, S.D., Turner, D.H.

Assembly

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

Entity

1. 5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3' (polymer, Thiol state: not present), 11 monomers, 3593.150 × 2 Da Detail

GACAAGUGUC A

Total weight

7186.3 Da

Max. entity weight

3593.15 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 63.6 %, Completeness: 4.9 %, Completeness (bb): 0.0 % Detail

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Polymer type: polyribonucleotide

	Total	1H	13C	15N	31P
All	4.9 % (9 of 184)	9.6 % (9 of 94)	0.0 % (0 of 74)	0.0 % (0 of 5)	0.0 % (0 of 11)
Suger, PO4	0.0 % (0 of 132)	0.0 % (0 of 66)	0.0 % (0 of 55)		0.0 % (0 of 11)
Nucleobase	17.3 % (9 of 52)	32.1 % (9 of 28)	0.0 % (0 of 19)	0.0 % (0 of 5)
Aromatic	10.4 % (5 of 48)	20.8 % (5 of 24)	0.0 % (0 of 19)	0.0 % (0 of 5)

1. RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')

GACAAGUGUC A

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')	natural abundance		1 mM
2	sodium chloride	natural abundance		80 mM
3	sodium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
7	RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')	natural abundance		1 mM
8	sodium chloride	natural abundance		80 mM
9	sodium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

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Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 37.2 %, Completeness (bb): 33.0 % Detail

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Polymer type: polyribonucleotide

	Total	1H	13C	15N	31P
All	37.2 % (137 of 368)	50.0 % (94 of 188)	19.6 % (29 of 148)	40.0 % (4 of 10)	45.5 % (10 of 22)
Suger, PO4	33.0 % (87 of 264)	50.0 % (66 of 132)	10.0 % (11 of 110)		45.5 % (10 of 22)
Nucleobase	48.1 % (50 of 104)	50.0 % (28 of 56)	47.4 % (18 of 38)	40.0 % (4 of 10)
Aromatic	47.9 % (46 of 96)	50.0 % (24 of 48)	47.4 % (18 of 38)	40.0 % (4 of 10)

1. RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')

GACAAGUGUC A

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')	natural abundance		1 mM
2	sodium chloride	natural abundance		80 mM
3	sodium phosphate	natural abundance		10 mM
4	EDTA	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.1

#	Name	Isotope labeling	Type	Concentration
7	RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')	natural abundance		1 mM
8	sodium chloride	natural abundance		80 mM
9	sodium phosphate	natural abundance		10 mM
10	EDTA	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

Hide sample codition

Release date

2010-07-01

Citation

RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA
Hammond, N.B., Tolbert, B.S., Kierzek, R., Turner, D.H., Kennedy, S.D.
Biochemistry (2010), 49, 5817-5827, PubMed 20481618 , DOI 10.1021/bi100332r , Abstract

Related entities 1. 5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3', : 1 entities Detail

Experiments performed 6 experiments Detail