BMRB Entry 26934

Name: Solution Structure of first stem-loop of Escherichia coli DsrA RNA
Published: 2018-06-26

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26934

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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:

Solution Structure of first stem-loop of Escherichia coli DsrA RNA

Deposition date:

2016-11-04

Original release date:

2018-06-26

Authors:

Wu, Pengzhi; Wu, Jihui; Shi, Yunyu

Citation:

Citation: Wu, Pengzhi; Liu, Xiaodan; Yang, Lingna; Sun, Yitong; Gong, Qingguo; Wu, Jihui; Shi, Yunyu. "The important conformational plasticity of DsrA sRNA for adapting multiple target regulation." Nucleic Acids Res. 45, 9625-9639 (2017).
PubMed: 28934467

Assembly members:

Assembly members:
RNA_(23-MER), polymer, 23 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Host organism: Escherichia coli Vector: puC19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(23-MER): GGACAUCAGAUUUCCUGGUG UCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	140
15N chemical shifts	27
1H chemical shifts	203

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (23-MER)	1

Entities:

Entity 1, RNA (23-MER) 23 residues - Formula weight is not available

1

G

A

C

A

U

C

A

G

A

2

U

C

U

G

U

G

3

U

C

Samples:

sample_1: RNA_(23-MER) 0.7 mM; sodium phosphate 10 mM; sodium chloride 50 mM

sample_2: RNA_(23-MER) 0.7 mM; sodium phosphate 10 mM; sodium chloride 50 mM

sample_3: RNA_(23-MER), [U-100% 13C; U-100% 15N], 0.7 mM; sodium phosphate 10 mM; sodium chloride 50 mM

sample_4: RNA_(23-MER), [U-100% 13C; U-100% 15N], 0.7 mM; sodium phosphate 10 mM; sodium chloride 50 mM

sample_conditions_1: ionic strength: 60 mM; pH: 6.5; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 60 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HNN-COSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_2
2D HCN	sample_4	isotropic	sample_conditions_2
3D HCCH-COSY	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

xwinnmr, Bruker Biospin - collection, processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker DMX 600 MHz
Varian Uniform NMR System 700 MHz