BMRB Entry 52428

Name: 116-nt Programmed Ribosome Frameshift (PRF) element of SARS-CoV-2
Published: 2024-07-29

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52428

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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:

116-nt Programmed Ribosome Frameshift (PRF) element of SARS-CoV-2

Deposition date:

2024-04-29

Original release date:

2024-07-29

Authors:

Hernandez-Marin, Maria; Cantero-Camacho, Angel; Lopez-Nunez, Sergio; Gallego, Jose

Citation:

Citation: Hernandez-Marin, Maria; Cantero-Camacho, Angel; Mena, Ignacio; Lopez-Nunez, Sergio; Garcia-Sastre, Adolfo; Gallego, Jose. "Sarbecovirus Programmed Ribosome Frameshift RNA element folding studied by NMR spectroscopy and comparative analyses" .

Assembly members:

Assembly members:
entity_1, polymer, 117 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: In vitro transcription Host organism: Not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGAACCCAUGCUUCAGUCAG CUGAUGCACAAUCGUUUUUA AACGGGUUUGCGGUGUAAGU GCAGCCCGUCUUACACCGUG CGGCACAGGCACUAGUACUG AUGUCGUAUACAGGGCU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	55
1H chemical shifts	48

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	116-nt PRF sequence of SARS-CoV-2	1

Entities:

Entity 1, 116-nt PRF sequence of SARS-CoV-2 117 residues - Formula weight is not available

The sequences experimentally analyzed in this study correspond to SARS-CoV-2 isolate Wuhan-Hu-1 (NCBI NC_045512). To obtain genomic numbering add 13,419 to the authors' sequence numbers.

1

G

A

C

A

U

G

2

C

U

C

A

G

U

C

A

G

3

C

U

G

A

U

G

C

A

C

A

4

A

U

C

G

U

A

5

A

C

G

U

G

6

C

G

U

G

U

A

G

U

7

G

C

A

G

C

G

U

C

8

U

A

C

A

C

G

U

G

9

C

G

C

A

C

A

G

C

10

A

C

U

A

G

U

A

C

U

G

11

A

U

G

U

C

G

U

A

U

A

12

C

A

G

C

U

Samples:

sample_1: 116-nt PRF sequence of SARS-CoV-2, [U-99% 13C; U-99% 15N], 107 uM; potassium phosphate 25 mM; potassium chloride 50 mM

sample_conditions_1: 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 HNN-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRFARM-Sparky v1.414 - collection, data analysis

TOPSPIN v3.6.1 - collection, data analysis

NMR spectrometers:

Bruker Avance 600 MHz