BMRB Entry 25781

Name: NMR Assignment and NMR Structure of CssA3 (top stem) of CssA thermometer
Published: 2016-07-26

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PDB ID: 2n6t
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25781
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR Assignment and NMR Structure of CssA3 (top stem) of CssA thermometer PubMed: 27369378

Deposition date: 2015-08-28 Original release date: 2016-07-26

Authors: Barnwal, Ravi; Godin, Kate; Varani, Gabriele; Loh, Edmund; Yip, Jordan; Tang, Christoph

Citation: Barnwal, Ravi; Loh, Edmund; Godin, Kate; Yip, Jordan; Lavender, Hayley; Tang, Christoph; Varani, Gabriele. "Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis" Nucleic Acids Res. 44, 9426-9437 (2016).

Assembly members:
CssA3_RNA_(42-MER), polymer, 42 residues, 13348.949 Da.

Natural source: Common Name: b-proteobacteria Taxonomy ID: 487 Superkingdom: Bacteria Kingdom: not available Genus/species: Neisseria meningitidis

Experimental source: Production method: in vitro transcription

Entity Sequences (FASTA):
CssA3_RNA_(42-MER): GGGUAGAGUAUAAUUAGUCU UCGGACUUCCUUAUACUUAU CC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	67
15N chemical shifts	14
1H chemical shifts	231

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (42-MER)	1

Entities:

Entity 1, RNA (42-MER) 42 residues - 13348.949 Da.

1

G

U

A

G

A

G

U

A

2

U

A

U

A

G

U

C

U

3

U

C

G

A

C

U

C

4

U

A

U

A

C

U

A

U

5

C

Samples:

sample_1: CssA3 RNA (42-MER)0.4 – 1.1 mM; CssA3 RNA (42-MER), 13C/15N-uniformly labeled, 0.4 – 1.1 mM; CssA3 RNA (42-MER), 13C/15N-AU labeled, 0.4 – 1.1 mM; CssA3 RNA (42-MER), partially deuterated, 0.4 – 1.1 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 280 K

sample_conditions_2: pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	anisotropic	sample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz
Agilent INOVA 900 MHz