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Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:uPsi RNA Packaging Signal Complex
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 1.0 mM unlabeled nucleocapsid protein, 1.0 mM A-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308 2 2D NOESY 1.2 mM unlabeled nucleocapsid protein, 1.2 mM G-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308 3 2D NOESY 0.8 mM unlabeled nucleocapsid protein, 0.8 mM U-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308 4 2D NOESY 0.8 mM unlabeled nucleocapsid protein, 0.8 mM C-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308 5 2D NOESY 1.2 mM unlabeled nucleocapsid protein, 1.2 mM unlabeled uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308 6 3D_13C-separated_NOESY 1.2 mM 15N, 13C-labeled nucleocapsid protein, 1.2 mM unlabeled uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0; 5mM NaCl, 0.1 mM ZnCl2 100% D2O 5 mM NaCl, 0.1 mM ZnCl2 7.0 ambient 308
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DRX 800 2 Bruker DMX 600
NMR Refinement Method Details Software 1H-1H distance restraints, Hydrogen-bond restraints, Torsion angle restraints, Inter-phosphate restraints The structures are based on a total of 1697 restraints. 680 are NOE-derived distance restraints, 608 are Hydrogen-bond restraints, 239 are torsion angle restraints and 170 are inter-phosphate restraints. XwinNMR
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 800 Conformers Submitted Total Number 20 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 collection XwinNMR BRUKER 2 processing NMRPipe Delaglio, F., Grzesiek. S., Vuister, G.W., Zhu, G., Pfeifer, J., & Bax, A. 3 data analysis NMRView 5 Johnson, B.A., Blevins, R.A. 4 refinement CYANA 2.1 Guntert, P., Mumenthaler, C. & Wuthrich, K.