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.
Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
1mM U2 snRNA-intron duplex; 10mM sodium phosphate
90% H2O/10% D2O
50mM sodium chloride
6.4
ambient
278
2
2D NOESY
1mM U2 snRNA-intron duplex; 10mM sodium phosphate
100% D2O
50mM sodium chloride
6.4
ambient
293
3
2D TOCSY
1mM U2 snRNA-intron duplex; 10mM sodium phosphate
100% D2O
50mM sodium chloride
6.4
ambient
293
4
DQF-COSY
1mM U2 snRNA-intron duplex; 10mM sodium phosphate
100% D2O
50mM sodium chloride
6.4
ambient
293
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
UNITYPLUS
720
2
Varian
UNITYPLUS
720
NMR Refinement
Method
Details
Software
torsion angle molecular dynamics followed by conjugate gradient minimization
A total of 191 distance restraints were used, not including the 40 hydrogen bond distances imposed. Including the 133 dihedral restraints applied in structure calculations, 353 total restraints were applied.
VNMR
NMR Ensemble Information
Conformer Selection Criteria
lowest energy structures that did not violate data from fluorescence experiments
Conformers Calculated Total Number
800
Conformers Submitted Total Number
9
Representative Model
2 (lowest energy structure that agreed best with experimental data)
Additional NMR Experimental Information
Details
This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to resolve some spectral overlap.