BMRB Entry 34777

Name: Structure of a symmetrical internal loop motif with three consecutive U:U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV2 genomic RNA
Published: 2023-09-04

Click here to enlarge.

PDB ID: 8bwt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34777
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of a symmetrical internal loop motif with three consecutive U:U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV2 genomic RNA

Deposition date:

2022-12-07

Original release date:

2023-09-04

Authors:

Voegele, J.; Duchardt-Ferner, E.; Schwalbe, H.; Woehnert, J.

Citation:

Citation: Voegele, J.; Duchardt-Ferner, E.; Bains, J.; Knezic, B.; Wacker, A.; Sich, C.; Goerlach, M.; Weigand, J.; Sponer, J.; Krepl, M.; Schwalbe, H.; Woehnert, J.. "Structure of a symmetrical internal loop motif with three consecutive U:U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV2 genomic RNA" .

Assembly members:

Assembly members:
entity_1, polymer, 26 residues, 8242.842 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: GGCGUUUUCGCUUCGGCGUU UACGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	88
15N chemical shifts	23
1H chemical shifts	128
31P chemical shifts	10

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 26 residues - 8242.842 Da.

1

G

C

G

U

C

G

2

C

U

C

G

C

G

U

3

U

A

C

G

C

Samples:

sample_1: RNA (26-MER) 830 uM; potassium phosphate 25 mM; potassium chloride 50 mM; D2O 5%

sample_2: RNA (26-MER), [13C,15N-A,U], 1 mM; potassium phosphate 25 mM; potassium chloride 50 mM; D2O 5%

sample_3: RNA (26-MER), [13C,15N-A,U], 1 mM; potassium phosphate 25 mM; potassium chloride 50 mM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_2	isotropic	sample_conditions_1
H56C56(C4N3)H optimized for H56	sample_2	isotropic	sample_conditions_1
H56C56(C4N3)H optimized for C56	sample_2	isotropic	sample_conditions_1
H(C)N aromatic	sample_3	isotropic	sample_conditions_1
H(C)N aliphatic	sample_3	isotropic	sample_conditions_1
H(C)P-CCH-TOCSY	sample_3	isotropic	sample_conditions_2
H(N)CO	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
HCC-TOCSY-CCH-E.COSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE 600 MHz
Bruker AVANCE 700 MHz
Bruker AVANCE 800 MHz
Bruker AVANCE 900 MHz