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Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 2 2D 1H-13C HSQC 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 3 2D 1H-13C HSQC 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 4 2D 1H-13C HSQC 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 5 2D 1H-13C HSQC 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 6 2D 1H-1H NOESY 1 mM UAUCG-linker 100% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 7 2D 1H-1H NOESY 0.5 mM U5-PBS-M2-NC 100% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 8 2D 1H-1H NOESY 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311 9 2D 1H-1H NOESY 1 mM UAUCG-linker 100% D2O 10mM Tris, 10mM NaCl 7.0 ambient 288 10 3D 1H-13C NOESY 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC 90% H2O/10% D2O 10mM Tris, 10mM Nacl 7.0 ambient 311
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker DMX 700
NMR Refinement Method Details Software distance geometry CYANA
NMR Ensemble Information Conformer Selection Criteria structures with acceptable covalent geometry Conformers Calculated Total Number 1000 Conformers Submitted Total Number 10 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 refinement CYANA Guntert, Mumenthaler and Wuthrich 2 data analysis CYANA Guntert, Mumenthaler and Wuthrich 3 processing CYANA Guntert, Mumenthaler and Wuthrich 4 refinement CYANA Johnson, One Moon Scientific 5 data analysis CYANA Johnson, One Moon Scientific 6 processing CYANA Johnson, One Moon Scientific 7 refinement CYANA Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 8 data analysis CYANA Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 9 processing CYANA Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax