2MKK | pdb_00002mkk

Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA

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	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-19, 0.4-0.6 mM 5'-UUUUA-3'-20, 100 mM sodium chloride-21, 50 mM sodium phosphate-22, 1 mM DTT-23, 1 mM magnesium sulfate-24	90% H2O/10% D2O	0.15	6.5	ambient atm	313
2	2D TROSY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-19, 0.4-0.6 mM 5'-UUUUA-3'-20, 100 mM sodium chloride-21, 50 mM sodium phosphate-22, 1 mM DTT-23, 1 mM magnesium sulfate-24	90% H2O/10% D2O	0.15	6.5	ambient atm	313
3	2D 1H-13C HSQC	0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12	90% H2O/10% D2O	0.15	6.5	ambient atm	313
4	2D 1H-13C HSQC aliphatic	0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12	90% H2O/10% D2O	0.15	6.5	ambient atm	313
5	2D 1H-13C HSQC aromatic	0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12	90% H2O/10% D2O	0.15	6.5	ambient atm	313
6	2D 1H-1H TOCSY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-25, 0.4-0.6 mM 5'-UUUUA-3'-26, 100 mM sodium chloride-27, 50 mM sodium phosphate-28, 1 mM DTT-29, 1 mM magnesium sulfate-30	100% D2O	0.15	6.5	ambient atm	313
7	2D 1H-1H NOESY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-25, 0.4-0.6 mM 5'-UUUUA-3'-26, 100 mM sodium chloride-27, 50 mM sodium phosphate-28, 1 mM DTT-29, 1 mM magnesium sulfate-30	100% D2O	0.15	6.5	ambient atm	313
8	3D trHNCA	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
9	3D trHN(CO)CA	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
10	3D trCBCA(CO)NH	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
11	3D trHNCACB	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
12	3D trHNCACO	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
13	3D trHNCO	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
14	3D HCCH-TOCSY	0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12	90% H2O/10% D2O	0.15	6.5	ambient atm	313
15	3D HCCH-TOCSY	0.4-0.6 mM [U-100% 13C; U-100% 15N] CPEB1RRM12-7, 0.4-0.6 mM 5'-UUUUA-3'-8, 100 mM sodium chloride-9, 50 mM sodium phosphate-10, 1 mM DTT-11, 1 mM magnesium sulfate-12	90% H2O/10% D2O	0.15	6.5	ambient atm	313
16	3D 1H-15N NOESY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-19, 0.4-0.6 mM 5'-UUUUA-3'-20, 100 mM sodium chloride-21, 50 mM sodium phosphate-22, 1 mM DTT-23, 1 mM magnesium sulfate-24	90% H2O/10% D2O	0.15	6.5	ambient atm	313
17	3D 1H-13C NOESY aliphatic	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
18	3D 1H-13C NOESY aromatic	0.4-0.6 mM [U-100% 13C; U-100% 15N; U-80% 2H] CPEB1RRM12-1, 0.4-0.6 mM 5'-UUUUA-3'-2, 100 mM sodium chloride-3, 50 mM sodium phosphate-4, 1 mM DTT-5, 1 mM magnesium sulfate-6	90% H2O/10% D2O	0.15	6.5	ambient atm	313
19	2D 13C-F1-filtered F2-filtered NOESY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-31, 0.4-0.6 mM 5'-CUUUA-3'-32, 100 mM sodium chloride-33, 50 mM sodium phosphate-34, 1 mM DTT-35, 1 mM magnesium sulfate-36	100% D2O	0.15	6.5	ambient atm	313
20	2D 1H-1H F1-13C-filtered F2-13C-edited NOESY	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-31, 0.4-0.6 mM 5'-CUUUA-3'-32, 100 mM sodium chloride-33, 50 mM sodium phosphate-34, 1 mM DTT-35, 1 mM magnesium sulfate-36	100% D2O	0.15	6.5	ambient atm	313
21	3D 13C-F1-edited F3-filtered NOESY HSQC	0.4-0.6 mM [U-100% 15N] CPEB1RRM12-31, 0.4-0.6 mM 5'-CUUUA-3'-32, 100 mM sodium chloride-33, 50 mM sodium phosphate-34, 1 mM DTT-35, 1 mM magnesium sulfate-36	100% D2O	0.15	6.5	ambient atm	313

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	900
2	Bruker	AVANCE	700
3	Bruker	AVANCE	600
4	Bruker	AVANCE	500

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	20
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	processing	TopSpin		Bruker Biospin
3	structure solution	CYANA		Guntert, Mumenthaler and Wuthrich
4	chemical shift assignment	Sparky		Goddard