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NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298 2 3D_13C-separated_NOESY 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298 3 3D_13C-separated_ROESY 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298 4 3D_15N-separated_NOESY 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298 5 4D_13C/15N-separated_NOESY 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298 6 HNCA-J 0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled 25mM Acetate buffer 25mM NaCl 6.5 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DMX 600 2 Bruker DRX 800
NMR Refinement Method Details Software distance geometry, simulated annealing XwinNMR
NMR Ensemble Information Conformer Selection Criteria target function Conformers Calculated Total Number 400 Conformers Submitted Total Number 20 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 collection XwinNMR 2.6 Burker 2 processing NMRPipe 1.0 Delaglio, Gresiek, Vuister, Zhu, Pfeifer, and Bax 3 data analysis NMRView 3.0 Johnson and Blevins 4 structure solution DYANA 1.5 Guntert, Mumenthaler and Wuthrich 5 refinement DYANA 1.5 Guntert, Mumenthaler and Wuthrich