2Z59
Complex Structures of Mouse Rpn13 (22-130aa) and ubiquitin
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | HNCACB, HNCA/HN(CO)CA | 0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
2 | 3D_15N-separated_NOESY | 0.6mM MmRpn13 U-15N; U-50% 2H; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
3 | 3D_15N-separated_NOESY | 0.6mM MmRpn13 U-15N, 13C; U-70% 2H; 0.6mM ubiquitin; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
4 | HSQC titration | 0.4mM MmRpn13 U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
5 | HSQC titration | 0.4mM ubiquitin U-15N; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
6 | HSQC titration | 0.4mM MmRpn13 U-13C; 20mM phosphate buffer; 30mM NaCl; 3mM DTT; 100% D2O | 100% D2O | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
High Ambiguity Driven protein-protein DOCKing | The strctures are based on interaction data such as chemical shift perturbation data resulting from NMR titration experiments and intermolecular NOE. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | 2006 | Frank Delaglio, Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer and Ad Bax |
2 | data analysis | XEASY | 1996 | Tai-he Xia and Christian Bartels |
3 | structure solution | HADDOCK | 1.3 | Cyril Dominguez, Rolf Boelens, Alexandre M.J.J.Bonvin |
4 | refinement | HADDOCK | 1.3 | Cyril Dominguez, Rolf Boelens, Alexandre M.J.J.Bonvin |