7KLR

Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	CBCACONH	550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
2	CBCANH	550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
3	3D (H)CCCONH-TOCSY	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
4	3D H(CC)(CO)NH-TOCSY	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
5	3D HCCH-TOCSY	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
10	3D NOESY	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
9	N HSQC	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
8	C HSQC	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
7	3D filtered intermolecular NOESY	900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
6	2D intra-peptide TOCSY	1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600
11	2D intra-peptide NOESY	1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2	95% H2O/5% D2O	150 mM	7.5	1 atm	298	Bruker AVANCE 600

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

NMR Refinement
Method	Details	Software
simulated annealing		ARIA

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	ARIA	2.3.2	Linge, O'Donoghue and Nilges
2	structure calculation	ARIA	2.3.2	Linge, O'Donoghue and Nilges
3	chemical shift assignment	CcpNmr Analysis	2.4.2	CCPN
4	peak picking	CcpNmr Analysis	2.4.2	CCPN

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.