BMRB Entry 25780

Name: Structure of CssA4 (bottom stem) of CssA thermometer
Published: 2016-07-26

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PDB ID: 2n6s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25780
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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:

Structure of CssA4 (bottom stem) of CssA thermometer

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:

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).
PubMed: 27369378

Assembly members:

Assembly members:
RNA_(36-MER), polymer, 36 residues, 11474.870 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: in vitro transcription

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(36-MER): GGAAUUUAUGAGUACCUUCG GAUACUUAUAGAUUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	76
15N chemical shifts	17
1H chemical shifts	215

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (36-MER)	1

Entities:

Entity 1, RNA (36-MER) 36 residues - 11474.870 Da.

1

G

A

U

A

U

G

2

A

G

U

A

C

U

C

G

3

G

A

U

A

C

U

A

U

A

4

G

A

U

C

Samples:

sample_1: CssA4 (36mer)0.4 – 1.1 mM; CssA4 (36mer), 13C/15N-uniformly labeled, 0.4 – 1.1 mM; CssA4 (36mer), 13C/15N-AU labeled, 0.4 – 1.1 mM; CssA4 (36mer), 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-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	isotropic	sample_conditions_1
ARTSY	sample_1	anisotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

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

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

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

NMR spectrometers:

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