1YNE

NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY2 mM edited apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm313
22D TOCSY2 mM edited apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm313
33D_13C-separated_NOESY1.5 mM edited apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm313
4DQF-COSY2 mM edited apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm313
5HNN-COSY1.5 mM edited apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm278
6HCCH-TOCSY1.5 mM edited apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O and only 99.98% D2O90% H2O, 10% D2O and only 99.98% D2O10 mM Na2HPO45.81 atm313
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX500
2BrukerDRX600
3BrukerAVANCE900
NMR Refinement
MethodDetailsSoftware
CYANA & AMBER7calculation in vacuum conditionCYANA
NMR Ensemble Information
Conformer Selection Criteriaback calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
Conformers Calculated Total Number50
Conformers Submitted Total Number20
Representative Model18 (closest to the average)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionCYANA2.0Guentert, P.
2collectionXwinNMR2004Bruker
3data analysisSparky2002Goddard, T. D. and Kneller, D. G.
4data analysisX-EASY2001Bartels, C.
5refinementAmber7Ponder, J.W. and Case, D.A.