BMRB Entry 19018

Name: NMR structure of E. coli ribosomela decoding site with apramycin
Published: 2013-03-13

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PDB ID: 2m4q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19018
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of E. coli ribosomela decoding site with apramycin PubMed: 23416053

Deposition date: 2013-02-10 Original release date: 2013-03-13

Authors: Puglisi, Joseph; Tsai, Albert; Marshall, R. Andrew; Viani, Elisabetta

Citation: Tsai, Albert; Uemura, Sotaro; Johansson, Magnus; Puglisi, Elisabetta Viani; Marshall, R. Andrew; Aitken, Colin Echeverria; Korlach, Jonas; Ehrenberg, Mans; Puglisi, Joseph. "The impact of aminoglycosides on the dynamics of translation elongation." Cell Rep. 3, 497-508 (2013).

Assembly members:
RNA, polymer, 27 residues, 132.116 Da.
APRAMYCIN, non-polymer, 539.577 Da.

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
RNA: GGCGUCACACCUUCGGGUGA AGUCGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	256
15N chemical shifts	101
1H chemical shifts	262
31P chemical shifts	27

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1
2	APRAMYCIN_1	2
3	APRAMYCIN_2	2
4	APRAMYCIN_3	2

Entities:

Entity 1, RNA 27 residues - 132.116 Da.

1

G

C

G

U

C

A

C

A

C

2

C

U

C

G

U

G

A

3

A

G

U

C

G

C

Entity 2, APRAMYCIN_1 - C21 H41 N5 O11 - 539.577 Da.

1

AM2

Samples:

sample_1: RNA, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; APRAMYCIN0.5 – 1 mM; H2O 90%; D2O 10%

sample_2: RNA0.5 – 1 mM; APRAMYCIN0.5 – 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR, Brunger - refinement

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz