2KMJ | pdb_00002kmj

High resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4	90% H2O/10% D2O	75	6.2	ambient	283
2	2D 1H-13C HSQC	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
3	2D 1H-1H TOCSY	0.65 mM UUCG-TAR-9, 5.2 mM Pyrimidinylpeptide-10, 50 mM potassium chloride-11, 25 mM potassium phosphate-12, 90% H2O / 10% D2O	90% H2O/10% D2O	75	6.2	ambient	298
4	2D 1H-1H NOESY	0.65 mM UUCG-TAR-9, 5.2 mM Pyrimidinylpeptide-10, 50 mM potassium chloride-11, 25 mM potassium phosphate-12, 90% H2O / 10% D2O	90% H2O/10% D2O	75	6.2	ambient	298
5	2D 1H-1H NOESY	0.65 mM UUCG-TAR-13, 5.2 mM Pyrimidinylpeptide-14, 50 mM potassium chloride-15, 25 mM potassium phosphate-16	100% D2O	75	6.2	ambient	298
6	3D HCCH-TOCSY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
7	3D HCCH-COSY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
8	3D 1H-15N NOESY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4	90% H2O/10% D2O	75	6.2	ambient	283
9	3D 1H-13C NOESY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
10	2D H(C)N	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
11	2D 1H-15N HSQC (2J)	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
12	2D 1H-13C HSQC	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
13	2D HNN-COSY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4	90% H2O/10% D2O	75	6.2	ambient	283
14	2D H5NN-COSY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
15	3D forward-directed HCC-TOCSY-CCH E.COSY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8	100% D2O	75	6.2	ambient	298
16	2D 1H-15N CPMG-NOESY	0.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4	90% H2O/10% D2O	75	6.2	ambient	283

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	900
2	Bruker	AVANCE	800
3	Bruker	AVANCE	700
4	Bruker	AVANCE	600
5	Bruker	DRX	600
6	Bruker	AVANCE	400

NMR Refinement
Method	Details	Software
simulated annealing		TopSpin

NMR Ensemble Information
Conformer Selection Criteria	Top-ranked ensemble
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (top-ranked ensemble)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	2.1	Bruker Biospin
2	processing	TopSpin	2.1	Bruker Biospin
3	data analysis	TopSpin	2.1	Bruker Biospin
4	chemical shift assignment	Sparky	3.114	Goddard
5	data analysis	Sparky	3.114	Goddard
6	peak picking	Sparky	3.114	Goddard
7	structure solution	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
8	refinement	ARIA	1.2	Linge, O'Donoghue and Nilges
9	refinement	HADDOCK	2.1	Dominguez, Boelens and Bonvin

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.