BMRB Entry 25164

Name: NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Published: 2014-10-14

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PDB ID: 2mtk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25164
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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:

NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

Deposition date:

2014-08-19

Original release date:

2014-10-14

Authors:

Bonneau, Eric; Legault, Pascale

Citation:

Citation: Bonneau, Eric; Legault, Pascale. "Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement." Biochemistry 53, 6264-6275 (2014).
PubMed: 25238589

Assembly members:

Assembly members:
RNA_(47-MER), polymer, 47 residues, 15118.061 Da.
MAGNESIUM ION, non-polymer, 24.305 Da.
WATER, water, 18.015 Da.

Natural source:

Natural source: Common Name: ascomycetes Taxonomy ID: 5141 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Neurospora crassa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pTZ19R

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(47-MER): GGACCUCCCGUCCUUGGACG GUCGAGCGAAAGCUUGUGAU UGGUCCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	368
13C chemical shifts	286
15N chemical shifts	39

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (47-MER)	1
2	MAGNESIUM ION_1	2
3	MAGNESIUM ION_2	2
4	MAGNESIUM ION_3	2
5	MAGNESIUM ION_4	2
6	MAGNESIUM ION_5	2
7	MAGNESIUM ION_6	2
8	water_1	3
9	water_2	3
10	water_3	3
11	water_4	3
12	water_5	3
13	water_6	3
14	water_7	3
15	water_8	3
16	water_9	3
17	water_10	3

Entities:

Entity 1, RNA (47-MER) 47 residues - 15118.061 Da.

1

G

A

C

U

C

G

2

U

C

U

G

A

C

G

3

G

U

C

G

A

G

C

G

A

4

A

G

C

U

G

U

G

A

U

5

U

G

U

C

G

Entity 2, MAGNESIUM ION_1 - Mg - 24.305 Da.

1

MG

Entity 3, water_1 - 18.015 Da.

1

HOH

Samples:

J345-1: J345-1, [U-100% 15N], 1.5 – 2.0 mM; KCl 50 mM; MgCl2 5 mM; H2O 90%; D2O 10%

J345-2: J345-2, [U-100% 13C; U-100% 15N], 2.0 mM; KCl 50 mM; MgCl2 5 mM; D2O 100%

J345-3: J345-3, [U-100% 13C; U-100% 15N], 2.0 mM; KCl 50 mM; MgCl2 5 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 288 K; pH: 6.5; ionic strength: 55 mM

sample_conditions_2: temperature: 298 K; pH: 6.5; ionic strength: 55 mM

Experiments:

Name	Sample	Sample state	Sample conditions
1D flip-back watergate 1H	J345-1	isotropic	sample_conditions_1
2D 1H-15N HSQC	J345-1	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	J345-1	isotropic	sample_conditions_1
3D 1H-15N NOESY	J345-1	isotropic	sample_conditions_1
2D 1H-13C HSQC	J345-2	isotropic	sample_conditions_2
3D 13C-edited HMQC-NOESY	J345-2	isotropic	sample_conditions_2
3D CT-HCCH-COSY	J345-2	isotropic	sample_conditions_2
3D HCCH-TOCSY	J345-2	isotropic	sample_conditions_2
3D 15N-edited NOESY-HSQC	J345-3	isotropic	sample_conditions_2
2D H(NC)-TOCSY-(C)H for guanosine residues	J345-3	isotropic	sample_conditions_2
2D 1H-13C HMQC	J345-2	isotropic	sample_conditions_2
2D 1H-15N MQ-(HC)N(C)H	J345-2	isotropic	sample_conditions_2
2D 1H-15N CPMG-NOESY	J345-1	isotropic	sample_conditions_1
2D HNN-COSY	J345-1	isotropic	sample_conditions_1

Software:

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

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

CCPNMR_suite, CCPN - chemical shift assignment, data analysis, peak picking

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

PyMol, Schrodinger - Structure analysis, Structure display

NMR spectrometers:

Varian Unity 600 MHz