9SXV | pdb_00009sxv

NMR structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.98 mM RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 900
2	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 800
3	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 20 mg/mL Pf1 phage	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 800
4	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 800
5	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 20 mg/mL Pf1 phage	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 800
6	3D qHCP	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
7	2D qHCP	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
8	2D P-FIDS	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
9	3D HCC-TOCSY-CCH-E.COSY	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 900
10	2D HNN-COSY	0.64 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
11	2D gamma HCCH	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
12	2D gamma HCNCH	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE II 600
13	2D gamma HCP	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
14	2D 1H-13C HSQC	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
15	2D 1H-15N HSQC	0.64 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600
16	2D HCN	0.64 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	95% H2O/5% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
17	3D forward directed HCCH-TOCSY	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 900
18	3D HCP	1.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS	100% D2O	13 mM	6.4	1 atm	308	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III HD	700
3	Bruker	AVANCE	800
4	Bruker	AVANCE	900
5	Bruker	AVANCE II	600

NMR Refinement
Method	Details	Software
simulated annealing		CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
3	structure calculation	ARIA		Linge, O'Donoghue and Nilges
7	structure calculation	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
4	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
5	processing	TopSpin		Bruker Biospin
6	data analysis	PALES		Zweckstetter and Bax

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.