9RME | pdb_00009rme

Hybrid NMR/Xray structure of SARS-CoV2 macrodomain (nsp3b) in complex with the sulfamoyl derivative of GS-441524

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D HNCA	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
2	3D HNCO	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
3	3D HN(CO)CA	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
4	3D HN(CA)CO	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
5	3D HNCACB	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
6	3D HCCH-TOCSY	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
7	3D HNHA	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800
8	3D-13C/15N-filtered NOESY-13C-HSQC	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 950
9	3D-13C/15N-filtered NOESY-15N-HSQC	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 950
10	2D w1-13C/15N-filtered NOESY	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 950
11	2D-w1,w2-13C/15N-filtered NOESY	1 mM [U-100% 13C; U-100% 15N] SARS-CoV2 nsp3 macrodomain (nsp3b), 1.1 mM sulfamoyl-GS441524, 25 mM TRIS, 150 mM sodium chloride, 3 mM TCEP	95% H2O/5% D2O	180 mM	6.5	atmospheric Pa	298	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	950
2	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing	The structure was obtained by taking the fixed coordinates of the X-ray structure 6W6Y and using the intermolecular NMR restraints to get the structure of the complex	CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	CARA		Keller and Wuthrich
2	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
3	processing	TopSpin		Bruker Biospin

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.