2LP1

The solution NMR structure of the transmembrane C-terminal domain of the amyloid precursor protein (C99)


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC-TROSY10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
23D HNCA10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
33D HNCACB10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
43D HN(CO)CA10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
53D HN(COCA)CB10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
63D HNCO10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
73D gnoesyNhsqc10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA90% H2O/10% D2O6.5ambient318
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAMX800
2BrukerAMX600
3VarianINOVA900
NMR Refinement
MethodDetailsSoftware
molecular dynamics, simulated annealingRESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING, FOLLOWED BY POWELL ENERGY MINIMIZATIONX-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number30
Representative Model1 (closest to the average)
Additional NMR Experimental Information
DetailsAll 2D and 3D experiments were TROSY based. For the RDC data collection, the TROSY/Semi-TROSY method was used.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionX-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clore
2refinementX-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clore
3data analysisNMRDrawLinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4data analysisSparky3.114Goddard
5chemical shift assignmentSparky3.114Goddard
6peak pickingSparky3.114Goddard
7processingNMRPipeLinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8geometry optimizationTALOSLinux9Cornilescu, Delaglio and Bax
9structure solutionTALOSLinux9Cornilescu, Delaglio and Bax
10data analysisProcheckNMR3.5.4Laskowski and MacArthur
11structure solutionProcheckNMR3.5.4Laskowski and MacArthur
12collectionTopSpin3Bruker Biospin