2LXC | pdb_00002lxc

Solution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
23D 1H-15N NOESY1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
33D 1H-15N TOCSY1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
42D 1H-13C HSQC aliphatic1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
52D 1H-13C HSQC aromatic1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
62D 1H-15N HSQC1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
73D HNCACB1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
83D HNCO1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
93D HCCH-TOCSY1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
103D HCCH-TOCSY1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
113D 1H-15N NOESY1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
123D 1H-13C NOESY aliphatic1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide90% H2O/10% D2O06.1ambient310
132D 1H-15N HSQC1 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide90% H2O/10% D2O06.1ambient310
142D 1H-15N HSQC1 mM [U-100% 13C; U-100% 15N] Get5, 2 mM Sgt2, 10 mM Bis-Tris, 50 mM L-arginine, 50 mM L-glutamic acid, 0.02 % sodium azide, 3.5 % polyacrylamide90% H2O/10% D2O06.1ambient310
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA600
2BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
simulated annealing, experimentally driven dockingSTRUCTURES OF ASYMMETRICALLY LABELED COMPLEX (SAMPLE_1 AND SAMPLE_3) WERE USED TO DETERMINE THE SEPERATE STRUCTURES OF GET5 OR SGT2, IN THEIR COMPLEX STATES. STRUCTURES ARE REFINED IN EXPLICIT WATER. AMBIGUOUS INTERACTION RESTRAINTS, RESIDUAL DIPOLAR COUPLINGS AND INTERMOLECULAR NOES WERE USED TO DOCK THE STRUCTURES OF GET5 AND SGT2, DETERMINED IN THEIR COMPLEX STATES. STRUCTURES ARE SELECTED FROM THE BEST SCORING CLUSTER BY HADDOCK SCORES AND REFINED IN WATER.VnmrJ
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionVnmrJVarian
2chemical shift assignmentAnalysisCCPN
3processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4data analysisTALOS+Cornilescu, Delaglio and Bax
5structure solutionARIA2.3Linge, O'Donoghue and Nilges
6refinementARIA2.3Linge, O'Donoghue and Nilges
7structure solutionHADDOCK2.1Alexandre Bonvin
8collectionTopSpinBruker Biospin
9data analysisPALESZweckstetter and Bax