2KKG

NMR structure of the octarepeat region of prion protein bound to pentosan polysulfate

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.5 mM [U-15N] octarepeats-1, 5 % [U-2H] D2O-2, 20 % [U-2H] DMSO-3, 20 mM pentosan polysulfate-4, 10 mM sodium acetate-5, 75 % H2O-6	95% H2O/5% D2O		5.0	ambient	298
2	2D 1H-13C HSQC	0.5 mM [U-13C; U-15N] octarepeats-13, 80 % [U-2H] D2O-14, 20 % [U-2H] DMSO-15, 20 mM pentosan polysulfate-16, 10 mM sodium acetate-17	100% D2O		5.0	ambient	298
3	3D CBCA(CO)NH	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
4	3D C(CO)NH	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
5	3D HNCA	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
6	3D HNCACB	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
7	3D HBHA(CO)NH	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
8	3D H(CCO)NH	0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12	95% H2O/5% D2O		5.0	ambient	298
9	3D HCCH-TOCSY	0.5 mM [U-13C; U-15N] octarepeats-13, 80 % [U-2H] D2O-14, 20 % [U-2H] DMSO-15, 20 mM pentosan polysulfate-16, 10 mM sodium acetate-17	100% D2O		5.0	ambient	298
10	3D 1H-15N NOESY	0.5 mM [U-15N] octarepeats-1, 5 % [U-2H] D2O-2, 20 % [U-2H] DMSO-3, 20 mM pentosan polysulfate-4, 10 mM sodium acetate-5, 75 % H2O-6	95% H2O/5% D2O		5.0	ambient	298
11	3D 1H-13C NOESY	0.5 mM [U-13C; U-15N] octarepeats-13, 80 % [U-2H] D2O-14, 20 % [U-2H] DMSO-15, 20 mM pentosan polysulfate-16, 10 mM sodium acetate-17	100% D2O		5.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600

NMR Refinement
Method	Details	Software
simulated annealing, molecular dynamics		ProcheckNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	40
Conformers Submitted Total Number	20
Representative Model	1 (n/a)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	geometry optimization	ProcheckNMR		Laskowski and MacArthur
2	data analysis	NMRView		Johnson, One Moon Scientific
3	peak picking	NMRView		Johnson, One Moon Scientific
4	structure solution	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
5	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
6	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.