1YMO

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


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 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 azide95% H2O,5% D2O or 100% D2O200 mM KCl6.3ambient283
22D 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 azide95% H2O,5% D2O or 100% D2O200 mM KCl6.3ambient293
32D 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 azide95% H2O,5% D2O or 100% D2O200 mM KCl6.3ambient283
42D 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 azide95% H2O,5% D2O or 100% D2O200 mM KCl6.3ambient293
52D 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% D2O200 mM KCl6.3ambient293
62D 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 azide95% H2O,5% D2O or 100% D2O200 mM KCl6.3ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX500
2BrukerDRX600
3BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
simulated annealingStructures 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 Criteriastructures with the lowest energy, no restraint violations, consistent with residual dipolar couplings
Conformers Calculated Total Number200
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsThe 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
#ClassificationVersionSoftware NameAuthor
1collectionXwinNMR2.6Bruker
2processingXwinNMR2.6Bruker
3data analysisAURELIA3.108Brunger
4structure solutionXPLOR-NIH1.0.6NIH
5refinementXPLOR-NIH1.0.6NIH