1FQZ
NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6 | 90% H2O/10% D2O | 8mM Na phosphate | 6.6 | ambient | 278 | |
2 | 2D NOESY | 1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6 | 100% D2O | 8mM Na phosphate | 6.6 | ambient | 278 | |
3 | 2D NOESY | 1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6 | 100% D2O | 8mM Na phosphate | 6.6 | ambient | 298 | |
4 | 2D NOESY | 8mM Na phosphate | 6.6 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DMX | 600 |
NMR Refinement | ||
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Method | Details | Software |
Using a motif-based approach, a model was constructed from X-ray and NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data. | Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry, structures with favorable non-bond energy |
Conformers Calculated Total Number | 1 |
Conformers Submitted Total Number | 1 |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.5 | Bruker |
2 | processing | NMRPipe | 1.7 | Delaglio |
3 | data analysis | Sparky | 3.66 | Goddard & Kneller |
4 | refinement | CHARMM | 25.2 | Brooks et al. |
5 | refinement | Insight II | 97.0 | MSI |