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NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O, 10% D2O and only 99.98% D2O 10 mM Na2HPO4 5.8 1 atm 313 2 2D TOCSY 2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O, 10% D2O and only 99.98% D2O 10 mM Na2HPO4 5.8 1 atm 313 3 3D_13C-separated_NOESY 2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O, 10% D2O and only 99.98% D2O 10 mM Na2HPO4 5.8 1 atm 313 4 DQF-COSY 2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O, 10% D2O and only 99.98% D2O 10 mM Na2HPO4 5.8 1 atm 313 5 HNN_COSY 1.5 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O/10% D2O 10 mM Na2HPO4 5.8 1 atm 278 6 HCCH-TOCSY 2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O 90% H2O, 10% D2O and only 99.98% D2O 10 mM Na2HPO4 5.8 1 atm 313
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DRX 500 2 Bruker DRX 600 3 Bruker AVANCE 900
NMR Refinement Method Details Software CYANA & AMBER7 calculation in vacuum condition CYANA
NMR Ensemble Information Conformer Selection Criteria back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy Conformers Calculated Total Number 50 Conformers Submitted Total Number 20 Representative Model 12 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution CYANA 2.0 Guentert, P. 2 collection XwinNMR 2004 Bruker 3 data analysis Sparky 2002 Goddard, T. D. and Kneller, D. G. 4 data analysis X-EASY 2001 Bartels, C. 5 refinement AMBER7 7 Ponder, J.W. and Case, D.A.