9SY4 | pdb_00009sy4

NMR structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop without restrained loop base pair


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY0.98 mM RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 900
22D 1H-13C HSQC0.2 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 800
32D 1H-13C HSQC0.2 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 50 mg/mL Pf1 phage95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 800
42D 1H-15N HSQC0.2 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 800
52D 1H-15N HSQC0.2 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 50 mg/mL Pf1 phage95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 800
63D qHCP1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
72D qHCP1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
82D P-FIDS1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
93D HCC-TOCSY-CCH-E.COSY1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 900
102D HNN-COSY0.64 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 600
112D gamma HCCH1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE III HD 700
122D gamma HCNCH1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE II 600
132D gamma HCP1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
142D 1H-13C HSQC1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
152D 1H-15N HSQC0.64 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE 600
162D HCN0.64 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS95% H2O/5% D2O13 mM6.41 atm308Bruker AVANCE III HD 700
173D forward directed HCCH-TOCSY1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 900
183D HCP1.26 mM [U-13C; U-15N] RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS100% D2O13 mM6.41 atm308Bruker AVANCE 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
2BrukerAVANCE III HD700
3BrukerAVANCE800
4BrukerAVANCE900
5BrukerAVANCE II600
NMR Refinement
MethodDetailsSoftware
simulated annealingCNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number10
Representative Model1 (closest to the average)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpinBruker Biospin
2chemical shift assignmentNMRFAM-SPARKYLee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
3structure calculationARIALinge, O'Donoghue and Nilges
4peak pickingNMRFAM-SPARKYLee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
5processingTopSpinBruker Biospin
6data analysisPALESZweckstetter and Bax
7structure calculationCNSBrunger, Adams, Clore, Gros, Nilges and Read