2DHS | pdb_00002dhs

Solution Structure of Nucleic Acid Binding Protein CUGBP1ab and its Binding Study with DNA and RNA

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
2	2D HSQC	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
3	3D HNCO	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
4	3D HNCA	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
5	3D HN(CO)CA	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
6	3D HNCACB	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
7	3D CBCA(CO)NH	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
8	3D HBHANH	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
9	3D HBHA(CO)NH	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
10	3D_15N-separated_NOESY	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
11	3D_13C-separated_NOESY	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
12	4D_13C-separated_NOESY	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
13	4D_13C/15N-separated_NOESY	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293
14	HNHA	0.8mM CUGBP1ab U-15N, 13C; 25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, and 0.125mM EDTA at pH 5.8, 90% H2O, 10% D2O	90% H2O/10% D2O	25mM sodium phosphate, 50mM NaCl, 0.25mM NaN3, 0.125mM EDTA	5.8	ambient	293

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

NMR Refinement
Method	Details	Software
simulated annealing molecular dynamics	The protein CUGBP1ab has total 187 residues (residues 1-187 of CUGBP1) including an N-terminus Histag-thrombin site (21 amino acids) and 20 amino acids in the C-terminus which is from the plasmid. The molecular weight of the CUGBP1ab is 25.4 kDa. The structures are based on a total of 4228 restraints, 3776 are NOE-derived distance donstraints, 324 dihedral angle restraints,128 distance restraints from hydrogen bonds.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	20
Conformers Submitted Total Number	7
Representative Model	1 (lowest energy)

Additional NMR Experimental Information

Details

The structure was determined using triple-resonance NMR spectroscopy. The both two domains RRM1 (RNA recognition motif) and RRM2 contain the same beta-alpha-beta-beta-alpha-beta topology as expected for RNA-recognition motif. The four beta strands form an anti parallel beta sheet. The two alpha helices are packed against the beta sheet. Other NMR experiments including 15N T1 and T2 and {1H}-15N steady state NOE, and titration with DNA and RNA, were carried out. the RRM1 shows more conformat on exchange than RRM2. The N-terminal region and the linker between the RRM1 and RRM2 show more flexibility than other regions. In addition, two loops L3 and L5 in RRM1 also demonstrate considerable flexibility and conformation exchange. The conformation exchange and flexibility in the RRM1 may be utilized in the recognition process by allowing different conformational states to be accessed and facilitating induced fit for complex forming. From the titration experiments,we found that the (GTC)3 and (GUCU)3 mainly bind the two central beta strands of the RRM1 and the linker of the RRM1 and RRM2 domains.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	2.3	Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Bax
2	data analysis	Sparky	3.112	T. D. Goddard and D. G. Kneller
3	structure solution	ARIA	2.0alpha	Michael Habeck, Wolfgang Rieping,Jens Linge and Michael Nilges
4	refinement	ARIA	2.0alpha	Michael Habeck, Wolfgang Rieping,Jens Linge and Michael Nilges