2KTR | pdb_00002ktr

NMR structure of p62 PB1 dimer determined based on PCS

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
2	2D 1H-15N HSQC	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
3	2D 1H-13C HSQC	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
4	2D 1H-13C HSQC	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
5	3D HNCA	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
6	3D HNCA	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
7	3D HN(CO)CA	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
8	3D HN(CO)CA	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
9	3D HNCACB	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
10	3D HNCACB	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
11	3D HNCO	0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298
12	3D HNCO	0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O	90% H2O/10% D2O	0.05	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	600

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing	In this work, the dimer structure of p62 PB1 was determined by using a rigid-body docking calculation based on the pseudo-contact shift. In the docking calculation, the coordinates of chain A were held fixed, whereas the coordinates of chain B were treated as a rigid body and set free to rotate and translate. The differences among the models are relative orientations between chain A and chain B, not each coordinates. In the calculation, monomer structures of DR and KE were docked each other based on the inter-subunit restraints from pseudo-contact shifts. The coordinates of DR and KE were generated from the monomer structure of DR (2kkc), using PyMOL software. For pseudo-contact shift restraints, we need a paramagnetic lanthanide ion fixed in the target protein. To fix a lanthanide ions to DR, we utilized the lanthanide binding peptide tag (LBT).The chain A represents LBT-DR, and chain B does KE. We collected the pseudo-contact shift restrains using LBT-DR/KE complex, while the docking calculations were performed using the coordinates without LBT.	Olivia

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Olivia		Masashi Yokochi
2	chemical shift assignment	Olivia		Masashi Yokochi
3	structure solution	X-PLOR NIH	2.9.20	Schwieters, Kuszewski, Tjandra and Clore
4	refinement	X-PLOR NIH	2.9.20	Schwieters, Kuszewski, Tjandra and Clore