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Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-15N HSQC 0.2 mM [U-99% 15N] CD2AP SH3-C, 1 mM Ubiquitin 90% H2O/10% D2O 0 6.0 1 atm 298 2 3D HNCO JNH, JCC, JCH, JCAHA 0.9 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 0.46 mM [U-99% 15N] Ubiquitin 90% H2O/10% D2O 0 6.0 1 atm 298 3 3D HNCO JNH, JCC, JCH, JCAHA 0.828 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.37 mM [U-99% 15N] Ubiquitin 90% H2O/10% D2O 0 6.0 1 atm 298 4 3D HNCO JNH, JCC, JCH, JCAHA 0.78 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin 90% H2O/10% D2O 0 6.0 1 atm 298 5 2D 1H-15N HSQC FILTERED DIPSAP 0.25 mM [U-99% 13C; U-99% 15N] CD2AP SH3-C, 1.75 mM [U-99% 15N] Ubiquitin 90% H2O/10% D2O 0 6.0 1 atm 298 6 2D 1H-15N HSQC 0.25 mM [U-99% 15N] Ubiquitin, 1 mM CD2AP SH3-C 90% H2O/10% D2O 0 6.0 1 atm 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian Uniform NMR System 600 2 Varian Uniform NMR System 800
NMR Refinement Method Details Software SIMULATED ANNEALING, MOLECULAR DYNAMICS DOCKING HADDOCK
NMR Ensemble Information Conformer Selection Criteria target function Conformers Calculated Total Number 200 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 refinement HADDOCK Alexandre Bonvin 2 refinement CNS/SCULPTOR Brunger, Adams, Clore, Gros, Nilges and Read 3 structure solution CNS/SCULPTOR Brunger, Adams, Clore, Gros, Nilges and Read 4 structure solution NMRView Johnson, One Moon Scientific 5 structure solution HADDOCK Alexandre Bonvin