Experiment: 8CQ1

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	500 uM [U-100% 15N] 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE III HD 800
8	NOESY[15N]-CPMG	500 uM [U-100% 15N] 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
10	NOESY[15N]-CPMG	350 uM [U-13C; U-15N] 5_SL4sh RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE III HD 800
2	3D 1H-13C NOESY aliphatic	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III 950
4	3D 13C,15N-filtered 1H-13C NOESY aromatic	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 800
3	3D 1H-13C NOESY aromatic	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE 600
5	3D 1H-13C NOESY aliphatic	500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE II 800
6	3D 1H-13C NOESY aromatic	500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE II 800
7	3D 13C,15N-filtered 1H-13C NOESY aliphatic	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 800
20	2D 1H-1H NOESY	1.8 mM 5_SL4sh RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE III 950
11	3D 1H-13C NOESY aromatic	350 uM [U-13C; U-15N] 5_SL4sh RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 800
12	3D 1H-13C NOESY aliphatic	350 uM [U-13C; U-15N] 5_SL4sh RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 600
13	1H,15N-IPAP-sofast-HMQC	200 uM [U-13C; U-15N]-Gua,Ura 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
14	1H,15N-IPAP-sofast-HMQC	200 uM [U-13C; U-15N]-Gua,Ury 5_SL4 RNA, 11.6 uM unlabeled Pf1 phage	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
15	1H,13C-IPAP-HSQC	200 uM [U-13C; U-15N]-Gua,Ura 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
16	1H,13C-IPAP-HSQC	200 uM [U-13C; U-15N]-Gua,Ury 5_SL4 RNA, 11.6 uM unlabeled Pf1 phage	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
17	1H,13C-IPAP-HSQC	200 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
18	1H,13C-IPAP-HSQC	200 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA, 11.6 mg/mL unlabeled Pf1 phage	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
21	lr HNN-COSY	500 uM [U-100% 15N] 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE III 950
22	HNN-COSY	500 uM [U-100% 15N] 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
23	3D HCCH-TOCSY	500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 800
24	3D HCCH-TOCSY	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 800
25	3D HCCH-TOCSY	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 600
26	3D HCCH-COSY	500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 600
27	3D HCCH-COSY	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE III HD 600
28	3D (H)CNC	500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
29	3D (H)CNC	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
30	2D Best-TROSY H(N)CO	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	283	Bruker AVANCE II 800
31	2D H5(C5)C4	500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA	95% H2O/5% D2O	100 mM	6.2	1 bar	298	Bruker AVANCE NEO 900

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE NEO	600
2	Bruker	AVANCE III HD	800
3	Bruker	AVANCE II	800
4	Bruker	AVANCE	600
5	Bruker	AVANCE III HD	700
6	Bruker	AVANCE III HD	600
7	Bruker	AVANCE III	950
8	Bruker	AVANCE NEO	900

NMR Refinement
Method	Details	Software
na		TopSpin
na		CARA
torsion angle dynamics		CYANA
molecular dynamics	refinement in water	ARIA

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (target function)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	CARA		Keller and Wuthrich
4	refinement	ARIA		Linge, O'Donoghue and Nilges

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.

8CQ1 | pdb_00008cq1

Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA

Prepare Data

Validate Data

Deposit Data

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Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA

8CQ1 | pdb_00008cq1