2MSC

NMR data-driven model of GTPase KRas-GDP tethered to a lipid-bilayer nanodisc


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-13C HMQC20 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]-1090% H2O/10% D2O0.1057.4ambient298
22D 1H-13C HMQC20 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)-2190% H2O/10% D2O0.1057.4ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
simulated annealingCNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number3000
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionCNSBrunger, Adams, Clore, Gros, Nilges and Read
2processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3processingNMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4structure solutionHADDOCKAlexandre Bonvin
5collectionTopSpinBruker Biospin
6data analysisSparkyGoddard
7structure solutionCHARMM-GUICHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im)
8refinementCNSBrunger, Adams, Clore, Gros, Nilges and Read