6UD0 | pdb_00006ud0

Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 800
8	2D 1H-15N HSQC	200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 800
2	2D 1H-15N HSQC	200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
9	2D 1H-15N HSQC	200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
3	2D 1H-15N HSQC	200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
10	2D 1H-15N HSQC	200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
4	2D 1H-15N HSQC	125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
5	2D 1H-15N HSQC	125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
6	2D 1H-15N HSQC	125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600
7	2D 1H-15N HSQC	125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride	93% H2O/7% D2O	0.1 M	5.8	1 atm	300	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
simulated annealing	Docking was carried out between the two proteins using rigid body simulated annealing with a flexible linker between diubiquitin domains. Initial structures were 3H7P and 2MJB for ubiquitin, and 1S1Q for Tsg101 UEV. Distal domain and Tsg101 backbone were fixed to 1S1Q position. Following initial docking, the lowest energy structure in each of the two clusters was used as input for refinement, with an ensemble number of 2.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (target function)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	9.5	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	collection	TopSpin	3.0	Bruker Biospin
5	peak picking	CcpNmr Analysis	2.4.2	CCPN
6	chemical shift assignment	CcpNmr Analysis	2.4.2	CCPN
7	refinement	X-PLOR NIH	2.51	Schwieters, Kuszewski, Tjandra and Clore
8	structure calculation	X-PLOR NIH	2.51	Schwieters, Kuszewski, Tjandra and Clore

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.