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 1RGO | pdb_00001rgo

Structural Basis for Recognition of the mRNA Class II AU-Rich Element by the Tandem Zinc Finger Domain of TIS11d


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D_15N-separated_NOESY0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO495% H2O, 5% D2020 mM KCl6.2ambient298
23D_13C-separated_NOESY0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
33D 13C F1-edited, F3-filtered NOESY0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
42D 13C double-half-filtered NOESY0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
5HNHA0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO495% H2O, 5% D2020 mM KCl6.2ambient298
6HNHB0.5 mM 15N-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO495% H2O, 5% D2020 mM KCl6.2ambient298
7HACAHB COSY0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
813C-{13CO} spin-echo difference CT-HSQC0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
913C-{15N} spin-echo difference CT-HSQC0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris-d11 pD 6.2; 20 mM KCl; 2.5 mM DTT-d10; 25 uM ZnSO4100% D2O20 mM KCl6.2ambient298
10IPAP-[1H-15N]-HSQC0.5 mM 15N,13C-TIS11d TZF; 0.5 mM 5'-UUAUUUAUU-3'; 10 mM Tris pH 6.2; 20 mM KCl; 2.5 mM DTT; 25 uM ZnSO4; 12 mg/mL Pf1 bacteriophage95% H2O/5% D2O20 mM KCl6.2ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
2BrukerDMX750
3BrukerAVANCE900
NMR Refinement
MethodDetailsSoftware
Individual zinc finger domains were created in DYANA and docked to UAUU (finger I) and UUAUU (finger II) using five rounds of simulated annealing in AMBER using distance and torsional restraints. Finger I/UAUU and Finger II/UUAUU complexes were connected to form TZF/UUAUUUAUU complexes and refined in AMBER with residual dipolar coupling restraints added. Calculations were then switched from in vacuo to Generalized Born continuum solvent model and one additional round of simulated annealing was performed.XwinNMR
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionXwinNMRvariousBruker
2processingNMRPipeDelaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer J.; Bax, A.
3data analysisNMRView5.0Johnson, B. A. & Blevins, R. A.
4data analysisSANEDuggan, B. M.
5structure solutionDYANA1.5Guntert, P.; Mumenthaler, C.; Wuthrich, K.
6structure solutionAmber8Case, D. A., et al.
7refinementAmber8Case, D. A., et al.