2MSC
NMR data-driven model of GTPase KRas-GDP tethered to a lipid-bilayer nanodisc
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HMQC | 20 mM TRIS-1, 100 mM sodium chloride-2, 2 mM TCEP-3, 5 mM MgCl2-4, 0.6 mM U-15N, Ile C-delta-13C K-Ras-5, 0.6 mM membrane scaffold protein-6, 0.6 mM GUANOSINE-5'-DIPHOSPHATE-7, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-8, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-9, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-10 | 90% H2O/10% D2O | 0.105 | 7.4 | ambient | 298 | |
2 | 2D 1H-13C HMQC | 20 mM TRIS-11, 100 mM sodium chloride-12, 2 mM TCEP-13, 5 mM Magnesium-14, 0.6 mM U-15N, Ile C-delta-13C K-Ras-15, 0.6 mM membrane scaffold protein-16, 0.6 mM GUANOSINE-5'-DIPHOSPHATE-17, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-18, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-19, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-20, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-21 | 90% H2O/10% D2O | 0.105 | 7.4 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 3000 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | structure solution | HADDOCK | Alexandre Bonvin | |
5 | collection | TopSpin | Bruker Biospin | |
6 | data analysis | Sparky | Goddard | |
7 | structure solution | CHARMM-GUI | CHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im) | |
8 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read |