6CC9
NMR data-driven model of GTPase KRas-GMPPNP:Cmpd2 complex tethered to a 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, 1H-15N TROSY | 0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC | 90% H2O/10% D2O | 100 mM NaCl mM | 7.4 | ambient atm | 298 | Bruker AVANCE 800 |
2 | 2D 1H-13C HMQC, 1H-15N TROSY | 0.2 mM U-15N, Ile, Leu C-delta-13C, Val C-gamma-13C GTPase KRas isoform b, 0.4 mM Membrane Scaffold Protein, 1 mM Cmpd2, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP, 12 mM DOPC, 3.2 mM DOPS, 0.8 mM PE-MCC | 90% H2O/10% D2O | 100 mM NaCl mM | 7.4 | ambient atm | 298 | Bruker AVANCE 800 |
3 | 3D_15N-separated_NOESY | 0.2 mM [U-15N] GTPase KRas isoform b, 1 mM Cmpd2, 100 mM sodium chloride, 20 mM TRIS, 5 mM magnesium chloride, 2 mM TCEP, 0.2 mM GMPPNP | 90% H2O/10% D2O | 100 mM NaCl mM | 7.4 | ambient atm | 298 | Bruker AVANCE 800 |
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 | 10 structures for lowest energy |
Conformers Calculated Total Number | 3000 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | HADDOCK modelling consists of (I) rigid-body docking, (II) a semi-flexible refinement stage, and (III) final refinement in explicit solvent (final gentle water). The starting structure is 2MSE. Distance restraints are based on PRE and NOE. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | Brunger A. T. et.al. | |
2 | structure calculation | HADDOCK | Bonvin | |
3 | chemical shift assignment | SPARKY-NMRFAM | Goddard. et. al. |