9FM4 | pdb_00009fm4

Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant

SOLUTION NMR - SOLUTION SCATTERING

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	283	Bruker AVANCE III HD 600
2	2D 1H-15N TROSY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	283	Bruker AVANCE III HD 600
3	3D HNN-COSY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	283	Bruker AVANCE III HD 600
4	3D HNCO	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	283	Bruker AVANCE III HD 600
5	2D 1H-13C HSQC	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	283	Bruker AVANCE III HD 600
6	2D 1H-1H NOESY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
7	2D 1H-15N TROSY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
8	2D 1H-15N HSQC NH2 only	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
9	3D HNCO	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
10	2D 1H-13C HSQC	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
11	2D 1H-15N HSQC 2J	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
12	2D 1H-13C HSQC LR	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
13	2D 1H-1H NOESY	700 uM [U-13C; U-15N]-Cyt s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 700
14	2D 1H-15N TROSY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
15	3D HNCO	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
16	2D 1H-13C HSQC LR	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
17	2D 1H-13C HSQC	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
18	2D 1H-13C HSQC	1700 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE NEO 900
19	2D 1H-13C HSQC	150 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 700
20	2D 1H-13C HSQC	150 uM [U-13C; U-15N]-Ade; U[U-13C; U-15N]-Ura s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
21	2D 1H-13C HSQC	200 uM [U-13C; U-15N]-Cyt s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
22	3D HCN	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
23	2D HCCNH	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
24	3D TROSY-HCCH-COSY	1700 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
25	3D-NOESY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
26	4D-HMQC-NOESY-HMQC	1700 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE NEO 900
27	3D HCCH-TOCSY	1700 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
28	3D fw-HCCH-TOCSY	150 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
29	3D fw-HCCH-TOCSY	150 uM [U-13C; U-15N]-Ade; U[U-13C; U-15N]-Ura s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
30	3D fw-HCCH-TOCSY	200 uM [U-13C; U-15N]-Cyt s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
31	2D CN-HSQC	1700 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III 800
32	2D 1H-15N CPMG NOESY	250 uM [U-100% 13C; U-100% 15N] s2m Delta_short RNA, 25 mM dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate, 50 mM potassium chloride	95% H2O/5% D2O	75 mM	6.2	1 atm	298	Bruker AVANCE III HD 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	600
2	Bruker	AVANCE III	800
3	Bruker	AVANCE III HD	800
4	Bruker	AVANCE III	700
5	Bruker	AVANCE NEO	900

NMR Refinement
Method	Details	Software
molecular dynamics

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
2	structure calculation	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
3	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
4	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
5	collection	TopSpin		Bruker Biospin
6	data analysis	TopSpin		Bruker Biospin
7	processing	TopSpin		Bruker Biospin

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9FM4 | pdb_00009fm4

Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant

9FM4 | pdb_00009fm4