2RN1

Liquid crystal solution structure of the kissing complex formed by the apical loop of the HIV TAR RNA and a high affinity RNA aptamer optimized by SELEX

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	1.1mM TAR, 1.1mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	90% H2O/10% D2O	60	6.6	ambient	283
2	2D 1H-1H NOESY	1.3mM TAR, 1.3mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
3	3D 1H-13C TROSY NOESY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
4	2D JNN-COSY	0.37mM [U-98% 13C; U-98% 15N] TAR, 0.74mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	90% H2O/10% D2O	60	6.6	ambient	278
5	3D HCCH-COSY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
6	3D HCCH-COSY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
7	3D HCN	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
8	3D HCN	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
9	2D intra base TOCSY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
10	3D 1H-13C TROSY NOESY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
11	2D intra base TOCSY	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
12	13C-1H spin state selective experiments	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
13	13C-1H spin state selective experiments	1.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
14	2D JNN-COSY	0.74mM TAR, 0.37mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	90% H2O/10% D2O	60	6.6	ambient	278
15	13C-1H spin state selective experiments	1.6mM TAR, 0.8mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298
16	13C-1H spin state selective experiments	0.5mM [U-98% 13C; U-98% 15N] TAR, 1.0mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide	100% D2O	60	6.6	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing	Xplor-NIH (Wimberly, 1992)	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	800
Conformers Submitted Total Number	17
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra, Clore
2	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra, Clore
3	chemical shift assignment	Felix	2000	Accelrys Software Inc.
4	processing	Felix	2000	Accelrys Software Inc.
5	data analysis	Insight II		Accelrys Software Inc.
6	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax
7	chemical shift assignment	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax
8	peak picking	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax
9	data analysis	Curves	5.3	Lavery, sklenar, 1989

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.