1YNE | pdb_00001yne

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

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2 mM edited 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 edited 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	1.5 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% D2O	90% H2O, 10% D2O and only 99.98% D2O	10 mM Na2HPO4	5.8	1 atm	313
4	DQF-COSY	2 mM edited 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 edited 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 and only 99.98% D2O	10 mM Na2HPO4	5.8	1 atm	278
6	HCCH-TOCSY	1.5 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% 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	18 (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	Amber	7	Ponder, J.W. and Case, D.A.

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.