1YMO | pdb_00001ymo

Solution structure of the P2b-P3 pseudoknot from human telomerase RNA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY (11echo and watergate)	~0.8 mM unlabeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	283
2	2D NOESY, 2D TOCSY (presat)	~0.8 mM unlabeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	293
3	2D 15N-HMQC,2D 15N-CPMG-NOESY, 2D JNN-HNN-COSY	~0.8 mM 13C,15N-fully labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	283
4	2D 13C-HSQC	~0.8 mM 13C,15N-fully labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	293
5	2D 13C-HSQC, 2D HCCH COSY, 3D HCCH-TOCSY, 2D 13C filtered/edited NOESYs	~0.8 mM 13C,15N-A labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	293
6	2D 13C-HSQC, 2D HCCH COSY, 3D HCCH-TOCSY, 2D 13C filtered/edited NOESYs	~0.8 mM 13C,15N-C labeled RNA, 10 mM sodium phosphate buffer, pH 6.3, 200 mM KCl, 50 uM EDTA, 0.2% sodium azide	95% H2O,5% D2O or 100% D2O	200 mM KCl	6.3	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500
2	Bruker	DRX	600
3	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing	Structures are based on 790 NOE-derived distance constraints, 210 dihedral angle restraints, 50 distance restraints from hydrogen bonds, and 20 H-C residual dipolar couplings. PDB entry PDB entry 2k96 is a better refined structure of entry 1ymo.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy, no restraint violations, consistent with residual dipolar couplings
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Additional NMR Experimental Information
Details	The same experiments were performed on all of the singly-labeled samples except for residual dipolar couplings which were only collected for the A- and G-only labeled samples.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.6	Bruker
2	processing	XwinNMR	2.6	Bruker
3	data analysis	AURELIA	3.108	Brunger
4	structure solution	XPLOR-NIH	1.0.6	NIH
5	refinement	XPLOR-NIH	1.0.6	NIH