BMRB Entry 34919

Name: Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant.
Published: 2025-06-24

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34919

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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:

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

Deposition date:

2024-06-05

Original release date:

2025-06-24

Authors:

Wirtz Martin, M.; Matzel, T.; Makowski, J.; Kensinger, A.; Herr, A.; Wacker, A.; Richter, C.; Jonker, H.; Evanseck, J.; Schwalbe, H.

Citation:

Citation: Wirtz Martin, M.; Matzel, T.. "Characterization of structure and dynamics of the apical stem loop of s2m from SCoV-2 Delta by NMR spectroscopy, validated by MD and SAXS" .

Assembly members:

Assembly members:
entity_1, polymer, 25 residues, 8068.861 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCACUCGGAGUACGAUCGA GUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	215
15N chemical shifts	48
1H chemical shifts	204

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 25 residues - 8068.861 Da.

1

G

C

A

C

U

C

G

A

2

G

U

A

C

G

A

U

C

G

A

3

G

U

G

C

Samples:

sample_1: s2m Delta_short RNA, [U-100% 13C; U-100% 15N], 250 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 50 mM

sample_2: s2m Delta_short RNA, [U-100% 13C; U-100% 15N], 1700 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 50 mM

sample_3: s2m Delta_short RNA, [U-100% 13C; U-100% 15N], 150 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 50 mM

sample_4: s2m Delta_short RNA, [U-13C; U-15N]-Ade; U[U-13C; U-15N]-Ura, 150 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 50 mM

sample_5: s2m Delta_short RNA, [U-13C; U-15N]-Cyt, 200 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 50 mM

sample_6: s2m Delta_short RNA, [U-13C; U-15N]-Cyt, 700 uM; dipotassium hydrogen orthophosphate/potassium dihydrogen phosphate 25 mM; potassium chloride 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
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D HNN-COSY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_2
3D HNCO	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC 2J	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC LR	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_3
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_3
3D HNCO	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC LR	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_3
3D HCN	sample_1	isotropic	sample_conditions_3
2D HCCNH	sample_1	isotropic	sample_conditions_3
3D TROSY-HCCH-COSY	sample_2	isotropic	sample_conditions_3
3D-NOESY	sample_1	isotropic	sample_conditions_3
4D-HMQC-NOESY-HMQC	sample_2	isotropic	sample_conditions_3
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_3
3D fw-HCCH-TOCSY	sample_3	isotropic	sample_conditions_3
3D fw-HCCH-TOCSY	sample_4	isotropic	sample_conditions_3
3D fw-HCCH-TOCSY	sample_5	isotropic	sample_conditions_3
2D CN-HSQC	sample_2	isotropic	sample_conditions_3
2D 1H-15N CPMG NOESY	sample_1	isotropic	sample_conditions_2

Software:

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

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

TopSpin, Bruker Biospin - collection, data analysis, processing

NMR spectrometers:

Bruker AVANCE III HD 600 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III HD 800 MHz
Bruker AVANCE III 700 MHz
Bruker AVANCE NEO 900 MHz