BMRB Entry 34909

Name: The 5-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
Published: 2024-06-20

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PDB ID: 9eow
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34909
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The 5-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH

Deposition date:

2024-03-15

Original release date:

2024-06-20

Authors:

Wacker, A.; Schwalbe, H.

Citation:

Citation: Toews, Sabrina; Wacker, Anna; Faison, Edgar; Duchardt-Ferner, Elke; Richter, Christian; Mathieu, Daniel; Bottaro, Sandro; Zhang, Qi; Schwalbe, Harald. "The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH" Nucleic Acids Res. ., .-. (2024).
PubMed: 38842942

Assembly members:

Assembly members:
entity_1, polymer, 29 residues, 9204.516 Da.

Natural source:

Natural source: Common Name: SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGUUUAUACCUUCCCAGGU AACAAACCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	245
15N chemical shifts	106
1H chemical shifts	258

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 29 residues - 9204.516 Da.

1

G

U

A

U

A

C

2

C

U

C

A

G

U

3

A

C

A

C

Samples:

sample_1: 5_SL1 15N, [U-15N], 150 uM; potassium phosphate 25 mM; KCl 50 mM

sample_2: 5_SL1 15N, [U-13C; U-15N], 400 uM; potassium phosphate 25 mM; KCl 50 mM

sample_3: 5_SL1 15N, A,C-13C, U-15N, 400 uM; potassium phosphate 25 mM; KCl 50 mM

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-JR[15N]	sample_1	isotropic	sample_conditions_1
NOESY[15N]-Imino	sample_1	isotropic	sample_conditions_1
HSQC[15N]-Amino	sample_1	isotropic	sample_conditions_1
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_1
TROSY[15N]	sample_1	isotropic	sample_conditions_1
HSQC[13C]-Aromaten	sample_2	isotropic	sample_conditions_2
TOCSY	sample_2	isotropic	sample_conditions_2
NOESY-JR[15N]-Amino	sample_2	isotropic	sample_conditions_2
TROSY[15N]	sample_2	isotropic	sample_conditions_2
HSQC[15N]-2J	sample_2	isotropic	sample_conditions_2
HSQC[15N]-Amino	sample_2	isotropic	sample_conditions_2
NOESY[15N]-Imino	sample_2	isotropic	sample_conditions_2
1H-JR[15N]	sample_2	isotropic	sample_conditions_2
HSQC[13C]-Aromaten	sample_2	isotropic	sample_conditions_2
TOCSY	sample_1	isotropic	sample_conditions_1
NOESY-JR[15N]-Amino	sample_1	isotropic	sample_conditions_1
HSQC[13C]-Aromaten	sample_3	isotropic	sample_conditions_3

Software:

TopSpin, Bruker Biospin - chemical shift assignment

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA, Linge, O'Donoghue and Nilges - refinement

NMRFAM-SPARKY, Wonghee Lee - peak picking

NMR spectrometers:

Bruker Bruker Avance III HD 800 MHz 800 MHz
Bruker Bruker Avance III HD 700 MHz 700 MHz
Bruker Bruker Avance I 600 MHz 600 MHz