1YMO
Solution structure of the P2b-P3 pseudoknot from human telomerase RNA
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
3 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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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 | |
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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 | |
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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 | ||||
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# | 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 |