BMRB Entry 17309

Name: Solution structure of coronaviral stem-loop 2 (SL2)
Published: 2010-12-02

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PDB ID: 2l6i
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17309
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of coronaviral stem-loop 2 (SL2) PubMed: 21382373

Deposition date: 2010-11-21 Original release date: 2010-12-02

Authors: Lee, Chul Won; Li, Lichun; Giedroc, David

Citation: Lee, Chul Won; Li, Lichun; Giedroc, David. "The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold." FEBS Lett. 585, 1049-1053 (2011).

Assembly members:
SL2, polymer, 16 residues, 135.128 Da.

Natural source: Common Name: coronavirus Taxonomy ID: 693996 Superkingdom: virus Kingdom: not available Genus/species: Alphacoronavirus Alphacoronavirus_1

Experimental source: Production method: in vitro transcription Host organism: Escherichia coli

Entity Sequences (FASTA):
SL2: GAUCUCUUGUAGAUCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	35
1H chemical shifts	123
31P chemical shifts	4

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	coronavirus stem-loop 2	1

Entities:

Entity 1, coronavirus stem-loop 2 16 residues - 135.128 Da.

1

G

A

U

C

U

C

U

G

U

2

A

G

A

U

C

A

Samples:

SL2_of_SARS_1: SL20.8 – 2 mM; potassium phosphate 10 mM; DSS 0.1 mM; D2O 100%

SL2_of_SARS_2: SL2, [U-13C; U-15N]-Ura, 0.8 – 2 mM; potassium phosphate 10 mM; DSS 0.1 mM; D2O 10%; H2O 90%

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 6.0; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	SL2_of_SARS_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	SL2_of_SARS_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	SL2_of_SARS_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	SL2_of_SARS_1	isotropic	sample_conditions_1
2D HNCCCH	SL2_of_SARS_1	isotropic	sample_conditions_1
2D H(CCN)H-TOCSY	SL2_of_SARS_1	isotropic	sample_conditions_1
2D HCN-HMQC	SL2_of_SARS_1	isotropic	sample_conditions_1
2D HCN-TROSY	SL2_of_SARS_1	isotropic	sample_conditions_1
2D HCNCH	SL2_of_SARS_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

SPARKY, Goddard - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz