2IHX
Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:uPsi RNA Packaging Signal Complex
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 800 |
2 | Bruker | DMX | 600 |
NMR Refinement | ||
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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 | |
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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 | ||||
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# | 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. |