2LPB | pdb_00002lpb

Structure of the complex of the central activation domain of Gcn4 bound to the mediator co-activator domain 1 of Gal11/med15

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	1-1.2 mM [U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
2	2D 1H-15N HSQC	2-2.4 mM Gal11, 1-1.2 mM [U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
3	3D CBCA(CO)NH	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
4	3D CBCA(CO)NH	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
5	3D HNCA	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
6	3D HNCA	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
7	3D HNCO	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
8	3D HNCO	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
9	3D HNCACB	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
10	3D HNCACB	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
11	3D 1H-15N NOESY	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
12	3D 1H-15N NOESY	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
13	3D 1H-13C NOESY aliphatic	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	100% D2O	150	6.5	ambient	298
14	3D 1H-13C NOESY aliphatic	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
15	3D 1H-13C NOESY aromatic	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	100% D2O	150	6.5	ambient	298
16	3D 1H-13C NOESY aromatic	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
17	3D C(CO)NH	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
18	3D C(CO)NH	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
19	3D H(CCO)NH	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
20	3D H(CCO)NH	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
21	2D 1H-13C HSQC aliphatic	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
22	2D 1H-13C HSQC aliphatic	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
23	2D 1H-13C HSQC aromatic	1-1.2 mM [U-13C; U-15N] Gal11, 2-2.4 mM Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298
24	2D 1H-13C HSQC aromatic	2-2.4 mM Gal11, 1-1.2 mM [U-13C; U-15N] Gcn4, 20 mM Sodium phosphate, 150 mM Sodium chloride, 1 mM PMSF, 5 mM DTT	90% H2O/10% D2O	150	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	900
2	Varian	INOVA	800
3	Varian	INOVA	600
4	Bruker	DMX	500

NMR Refinement
Method	Details	Software
simulated annealing		CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	13
Conformers Submitted Total Number	13
Representative Model	1 (n/a)

Additional NMR Experimental Information
Details	The authors state that the structures are arranged by energy, preceeding from lowest to highest, but there is no single representative structure. Binding of Gcn4 residues 101-134 to Gal11 residues 158-238 is best represented by the entire ensemble as Gcn4 binds in multiple orientations.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CNS	1.3	Brunger, Adams, Clore, Gros, Nilges and Read
2	data analysis	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	NMRView		Johnson, One Moon Scientific
4	structure solution	HADDOCK	2.1	Alexandre Bonvin
5	collection	VNMR		Varian
6	collection	TopSpin		Bruker Biospin
7	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read