Experiment: 6NOA

Solution Structure of the RNA element that recruits eIF3 to the 5'-UTR of c-Jun and regulates specialized translation initiation (apical loop)

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	1.0 mM [A,G-98% D3', 4', 5', 5"; C,U-98% D3', 4', 5', 5", 5] RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
2	2D 1H-1H NOESY	1.0 mM RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
3	2D 1H-1H TOCSY	1.0 mM RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
4	2D 1H-1H NOESY	1.0 mM RNA	90% H2O/10% D2O	20mM Sodium Phosphate	6.1	1 atm	278	Bruker AVANCE III 800
5	2D 1H-1H NOESY	1.0 mM RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
6	2D 1H-1H NOESY	1.0 mM RNA	90% H2O/10% D2O	20mM Sodium Phosphate	6.1	1 atm	278	Bruker AVANCE III 800
7	2D 1H-1H NOESY	1.0 mM [A,G-98% D3', 4', 5', 5"; C,U-98% D3', 4', 5', 5", 5] RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
11	3D 1H-13C NOESY	1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
10	2D 1H-15N HSQC	1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA	90% H2O/10% D2O	20mM Sodium Phosphate	6.1	1 atm	278	Bruker AVANCE II 600
9	2D 1H-13C HSQC	1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800
8	2D 1H-1H TOCSY	1.0 mM RNA	100% D2O	20mM Sodium Phosphate	6.1	1 atm	298	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	800
2	Bruker	AVANCE II	600

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	peak picking	Sparky		Goddard
4	peak picking	CcpNmr Analysis		CCPN
5	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	chemical shift assignment	TopSpin		Bruker Biospin