2K9Y

EphA2 dimeric structure in the lipidic bicelle at pH 5.0


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
22D 1H-13C HSQC3 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer95% H2O/5% D2O105AMBIENT313
33D HNCO3 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer95% H2O/5% D2O105AMBIENT313
43D HNCA3 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer95% H2O/5% D2O105AMBIENT313
53D HCCH-TOCSY3 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer95% H2O/5% D2O105AMBIENT313
63D 1H-15N NOESY3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
73D 1H-15N TOCSY3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
83D 1H-13C NOESY3 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer95% H2O/5% D2O105AMBIENT313
93D HNHB3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
103D HNHA3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
112D 1H-1H NOESY3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
1213C F1-filtered/F3-edited-NOESY1.5 mM [U-95% 13C; U-95% 15N] EphA2_TM 15N,13C, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer, 1.5 mM EphA2_TM100% D2O105AMBIENT313
1315N-T23 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
1415N-T13 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
1515N-NOE3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
162D 1H-1H TOCSY3 mM [U-95% 15N] EphA2_TM 15N, 96 mM [U-2H] DHPC, 24 mM [U-2H] DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer90% H2O/10% D2O105AMBIENT313
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUNITY600
2VarianINOVA600
NMR Refinement
MethodDetailsSoftware
TORSION ANGLE DYNAMICS, molecular dynamics, TORSION ANGLE DYNAMICSFirst 15 models represents Torsion Angle Dynamics with applied NMR restrains using CYANA software, Last two models (16 and 17) represents MD relaxation in the explicit hydrated DPPC bilayer with NMR restrains using GROMACS softwareNMRPipe
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number100
Conformers Submitted Total Number17
Representative Model1 (fewest violations)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1spectra processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2assignmentCARA1.5.5, 1.8Keller and Wuthrich
3structure calculationCYANA2.1Guntert, Mumenthaler and Wuthrich
4collectionVNMRVarian
5geometry optimizationGROMACS3.3.2Erik Lindahl
6refinementGROMACS3.3.2Erik Lindahl