Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE
SOLUTION NMR
NMR Experiment
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
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
500
2
Bruker
DMX
600
NMR Refinement
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
Conformer Selection Criteria
structures with acceptable covalent geometry, structures with favorable non-bond energy