1RGO

Structural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4	95% H2O, 5% D20	20 mM KCl	6.2	ambient	298
2	3D_13C-separated_NOESY	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
3	3D 13C F1-edited, F3-filtered NOESY	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
4	2D 13C double-half-filtered NOESY	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
5	HNHA	0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4	95% H2O, 5% D20	20 mM KCl	6.2	ambient	298
6	HNHB	0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4	95% H2O, 5% D20	20 mM KCl	6.2	ambient	298
7	HACAHB COSY	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
8	13C-{13CO} spin-echo difference CT-HSQC	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
9	13C-{15N} spin-echo difference CT-HSQC	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4	100% D2O	20 mM KCl	6.2	ambient	298
10	IPAP-[1H-15N]-HSQC	0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4; 12 mg/mL Pf1 bacteriophage	95% H2O/5% D2O	20 mM KCl	6.2	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	DMX	750
3	Bruker	AVANCE	900

NMR Refinement
Method	Details	Software
Individual zinc finger domains were created in DYANA and docked to UAUU (finger I) and UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance and torsional restraints. Finger I/UAUU and Finger II/UUAUU complexes were connected to form TZF/UUAUUUAUU complexes and refined in AMBER with residual dipolar coupling restraints added. Calculations were then switched from in vacuo to Generalized Born continuum solvent model and one additional round of simulated annealing was performed.		XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	various	Bruker
2	processing	NMRPipe		Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer J.; Bax, A.
3	data analysis	NMRView	5.0	Johnson, B. A. & Blevins, R. A.
4	data analysis	SANE		Duggan, B. M.
5	structure solution	DYANA	1.5	Guntert, P.; Mumenthaler, C.; Wuthrich, K.
6	structure solution	Amber	8	Case, D. A., et al.
7	refinement	Amber	8	Case, D. A., et al.

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.