2JY8

NMR structure of the ubiquitin associated (UBA) domain of p62 (SQSTM1) in complex with ubiquitin. RDC refined


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
23D 1H-15N TOCSY1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
33D 1H-15N NOESY1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
42D 1H-13C HSQC1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
53D HNCACB1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
63D CBCA(CO)NH1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
73D HCCH-TOCSY1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
83D 1H-13C NOESY1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
93D HNCO1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
103D HN(CA)CO1 mM [U-100% 13C; U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
112D 1H-15N HSQC-IPAP1 mM [U-100% 15N] protein, 50 mM potassium phosphate, 50 mM sodium chloride, 0.04 % sodium azide90% H2O/10% D2O7ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
simulated annealingIn the first stage, high temperature Cartesian dynamics was performed at 1000 K with a time step of 0.005 ps, for 20,000 steps, using the Verlet integrator. During the second cooling phase of the protocol, the temperature was reduced from 1000 K to 100 K in steps of 50 K, with a time step of 5 fs, over 40,000 steps during which the relative weighting of non-bonded energy terms were increased from 10% of their default values to their force field default. These initial structures were then refined with another 10000 cooling stepX-PLOR NIH
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number21
Representative Model1 (closest to the average)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionX-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clore
2collectionXwinNMR3.5Bruker Biospin
3processingXwinNMR3.5Bruker Biospin
4peak pickingCcpNMR1.0.10CCPN
5data analysisCcpNMR1.0.10CCPN
6chemical shift assignmentCcpNMR1.0.10CCPN
7geometry optimizationTALOSCornilescu, Delaglio and Bax
8refinementX-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clore