BMRB Entry 34991

Name: SARS-CoV-2 omicron stem-loop-II-motif (s2m_omicron)
Published: 2025-10-02

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PDB ID: 9qzj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34991
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

SARS-CoV-2 omicron stem-loop-II-motif (s2m_omicron)

Deposition date:

2025-04-23

Original release date:

2025-10-02

Authors:

Matzel, T.; Schwalbe, H.; Oxenfarth, A.; Wirtz Martin, M.

Citation:

Citation: Matzel, T.; Makowski, J.; Kensinger, A.; Oxenfarth, A.; Wirtz Martin, M.; Evanseck, J.; Schwalbe, H.. "Integrated NMR and MD structure and dynamics of the stem loop II motif (s2m) from the Omicron variant of SARS-CoV-2" RNA ., .-. (2025).
PubMed: 40973458

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 6037.649 Da.

Natural source:

Natural source: Common Name: SARS coronavirus Taxonomy ID: 2901879 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus Betacoronavirus pandemicum

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGUUCACCUACAGUGAACC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	116
15N chemical shifts	33
1H chemical shifts	185

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 19 residues - 6037.649 Da.

1

G

U

C

A

C

U

A

2

C

A

G

U

G

A

C

Samples:

sample_1: s2m_omicron 50 uM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_2: s2m_omicron, [U-13C; U-15N], 700 uM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_3: s2m_omicron, [U-13C; U-15N], 680 uM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_conditions_1: ionic strength: 125 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 125 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC NH2 only	sample_2	isotropic	sample_conditions_1
BEST-TROSY	sample_2	isotropic	sample_conditions_1
1H-15N CPMG-NOESY	sample_2	isotropic	sample_conditions_1
HNN-COSY	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_2
BEST-TROSY	sample_2	isotropic	sample_conditions_2
CNC	sample_3	isotropic	sample_conditions_2
1H-15N CPMG-NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_2
HCCNH	sample_2	isotropic	sample_conditions_2
3D HCN	sample_3	isotropic	sample_conditions_2
2D NOESY	sample_3	isotropic	sample_conditions_2
fw-HCCH-TOCSY	sample_3	isotropic	sample_conditions_2
2D NOESY	sample_2	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - collection, processing

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - structure calculation

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III HD 800 MHz
Bruker AVANCE III HD 600 MHz
Bruker AVANCE III HD 700 MHz
Bruker AVANCE NEO 600 MHz