BMRB Entry 52215

Name: SCoV-2 s2m delta
Published: 2024-08-05

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52215

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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:

SCoV-2 s2m delta

Deposition date:

2023-11-24

Original release date:

2024-08-05

Authors:

Matzel, Tobias; Wirtz Martin, Maria

Citation:

Citation: Matzel, Tobias; Wirtz Martin, Maria; Herr, Alexander; Wacker, Anna; Richter, Christian; Sridhar, Sreeramulu; Schwalbe, Harald. "NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2" RNA 30, 779-794 (2024).
PubMed: 38565242

Assembly members:

Assembly members:
entity_1, polymer, 45 residues, Formula weight is not available

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 Vector: pHDV_s2m_delta

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGUUCACCGAGGCCACUCGG AGUACGAUCGAGUGUACAGU GAACC

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	276
15N chemical shifts	123
1H chemical shifts	418

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	s2m delta	1

Entities:

Entity 1, s2m delta 45 residues - Formula weight is not available

1

G

U

C

A

C

G

A

2

G

C

A

C

U

C

G

3

A

G

U

A

C

G

A

U

C

G

4

A

G

U

G

U

A

C

A

G

U

5

G

A

C

Samples:

sample_1: s2m delta, [U-13C; U-15N], 400 uM; D2O, [U-2H], 5%; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 95%

sample_2: s2m delta, [U-13C; U-15N], 640 uM; D2O, [U-2H], 100%; potassium chloride 50 mM; potassium phosphate 25 mM

sample_3: s2m delta, [U-13C; U-15N]-Ade,Cyt, 290 uM; D2O, [U-2H], 100%; potassium chloride 50 mM; potassium phosphate 25 mM

sample_4: s2m delta, [U-13C; U-15N]-Gua,Ura, 360 uM; D2O, [U-2H], 100%; potassium chloride 50 mM; potassium phosphate 25 mM

sample_5: s2m delta 400 uM; D2O, [U-2H], 5%; potassium chloride 50 mM; potassium phosphate 25 mM; H2O 95%

sample_conditions_1: pH: 6.2; temperature: 283 K

sample_conditions_2: pH: 6.2; temperature: 298 K

sample_conditions_3: pH: 6.2; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
JR NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-15N BEST-TROSY	sample_1	isotropic	sample_conditions_1
HNN COSY	sample_1	isotropic	sample_conditions_1
JR NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_2
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_2
HNN COSY	sample_1	isotropic	sample_conditions_2
HCCNH-TOCSY	sample_1	isotropic	sample_conditions_2
CPMG-NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_3
3D HCN	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_3
3D fwHCCH-TOCSY	sample_4	isotropic	sample_conditions_3
3D fwHCCH-TOCSY	sample_3	isotropic	sample_conditions_3
3D fwHCCH-TOCSY	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_3
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_3
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_3
2D xfilter NOESY	sample_4	isotropic	sample_conditions_3
2D xfilter NOESY	sample_3	isotropic	sample_conditions_3
3D HCN	sample_1	isotropic	sample_conditions_3
HCCNH-TOCSY	sample_1	isotropic	sample_conditions_3
4D 13C-separated NOESY	sample_2	isotropic	sample_conditions_3

Software:

NMRFAM-SPARKY v1.470 - chemical shift assignment, peak picking

TOPSPIN vvarious versions - collection, processing

LOGS - collection

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 700 MHz
Bruker AVANCE III 950 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 600 MHz
Bruker AVANCE NEO 900 MHz