6GZK

Solution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	NOESY	1.2 mM unlabeled TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	100% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	283	Bruker AVANCE 950
2	3D 1H-13C NOESY aromatic	1.2 mM [U-13C; U-15N] TMR-3_48nt, 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 950
3	3D 1H-13C NOESY aliphatic	1.2 mM [U-13C; U-15N] TMR-3_48nt, 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 950
13	3D f1-13C,15N filtered 1H-13C NOESY aliphatic	1.2 mM [U-13C; U-15N] TMR-3_48nt, 1.4 mM unlabeled 5-TAMRA	100% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 900
4	3D f1-13C,15N filtered 1H-13C NOESY aromatic	1.2 mM [U-13C; U-15N]-Ade TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 900
5	3D 1H-13C NOESY aliphatic	1.2 mM [U-13C; U-15N]-Ade,Cyt TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	100% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 900
9	3D 1H-13C NOESY aromatic	1.2 mM [U-13C; U-15N]-Gua,Ura TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 900
8	3D 1H-13C NOESY aliphatic	1.2 mM [U-13C; U-15N]-Gua,Ura TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	100% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 950
7	f1,f2 filter NOESY	1.2 mM [U-13C; U-15N] TMR-3_48nt, 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 900
10	HNN-COSY	1.2 mM [U-15N] TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 600
11	SELLR HNN-COSY	1.2 mM [U-15N] TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 600
12	Amino HNN-COSY	1.2 mM [U-15N] TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	298	Bruker AVANCE 600
14	15N-1H CPMG NOESY	1.2 mM [U-15N] TMR3 (48-MER), 1.4 mM unlabeled 5-TAMRA	95% H2O/5% D2O	130 mM Na-Glutamate, 10 mM NaCl mM	7.2	1 bar	283	Bruker AVANCE 900

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
4	Bruker	AVANCE	900
5	Bruker	AVANCE	950

NMR Refinement
Method	Details	Software
torsion angle dynamics		CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CYANA	3.97	Guntert, Mumenthaler and Wuthrich
2	structure calculation	CYANA	3.97	Guntert, Mumenthaler and Wuthrich
3	processing	TopSpin		Bruker Biospin
4	chemical shift assignment	CARA		Keller and Wuthrich
5	peak picking	CARA		Keller and Wuthrich

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 R01GM133198.