1KRI

NMR Solution Structures of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain without Ligand

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	HSQC	1 mM EcVP8(46-231) U-15N	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
2	HNCA	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
3	HN(CO)CA	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
4	HNCACB	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
5	HN(CO)CACB	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
6	HNCO	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
7	HN(CA)CO	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
8	HCCCONH	1 mM EcVP8(46-231) U-15N, 13C, 2D	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
9	HSQC	0.1 mM EcVP8(46-231) U-15N-ile or U-15N-leu or U-15N-phe or U-15N-tyr or U-15N-val	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
10	HNHA	1 mM EcVP8(46-231) U-15N	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
11	HNHB	1 mM EcVP8(46-231) U-15N	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
12	3D-15N-separated TOCHSQC	1 mM EcVP8(46-231) U-15N	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
13	HCCH-TOCSY	1 mM EcVP8(46-231) U-15N, 13C	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
14	13C-HSQC	1 mM EcVP8(46-231) U-10% 13C	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
15	2D-D2O-TOCSY	1 mM EcVP8(46-231)	100% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
16	3D-13C-separated NOESY	1 mM EcVP8(46-231) U-15N, 13C	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
17	3D-15N-separated NOEHSQC	1 mM EcVP8(46-231) U-15N	90% H2O/10% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298
18	2D-D2O-NOESY	1 mM EcVP8(46-231)	100% D2O	20 mM NaPO4, 10 mM NaCl, 0.02% Na azide	7.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITY	500
2	Bruker	AVANCE	600
3	Varian	INOVA	750

NMR Refinement
Method	Details	Software
simulated annealing	The models are based on a total of 1993 constraints (12.5 constraints per residue): 1793 NOE-derived distance constraints; 116 TALOS-derived dihedral angle constraints; and 84 hydrogen bond constraints, based on the identification of slow exchange amide protons in D2O NOESY and TOCSY experiments, on characteristic NOE patterns for alpha-helices and beta-sheets, and on the proximity and orientation of potential hydrogen bond partners in annealed structures. The final set of 20 structures contains no violations of NOE distance constraints greater than 0.15 angstroms and no violations of dihedral angle constraints greater than 5 degrees.	PROSA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	25
Conformers Submitted Total Number	20
Representative Model	1 (least restraint violations)

Additional NMR Experimental Information
Details	The N-terminal 19 residues (A46 to V64 of VP4) and the C-terminal 7 residues (P225 to R231 of VP4) are disordered and are not included in the models.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	PROSA	3.7	Guntert, P., Dotsch, V., Wider, G., Wuthrich, K.
2	data analysis	XEASY	1.3.13	Bartels, C., Xia, T.-H., Billeter, M., Guntert., P., Wuthrich, K.
3	data analysis	DYANA	1.5	Guntert, P., Murmenthaler, C., Wuthrich, K.
4	data analysis	TALOS		Cornilescu, G., Delaglio, F., Bax, A.
5	structure solution	CNS	1.0	Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.
6	refinement	CNS	1.0	Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.

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.