BMRB Entry 25655

Name: NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Published: 2015-07-03

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PDB ID: 2n3r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25655
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement PubMed: 26124200

Deposition date: 2015-06-09 Original release date: 2015-07-03

Authors: Bonneau, Eric; Girard, Nicolas; Lemieux, Sebastien; Legault, Pascale

Citation: Bonneau, Eric; Girard, Nicolas; Lemieux, Sebastien; Legault, Pascale. "The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure" RNA 21, 1621-1632 (2015).

Assembly members:
RNA_(62-MER), polymer, 62 residues, 20022.115 Da.
MAGNESIUM ION, non-polymer, 24.305 Da.
WATER, water, 18.015 Da.

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

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

Entity Sequences (FASTA):
RNA_(62-MER): GCAGCAGGGAACUCACGCUU GCGUAGAGGCUAAGUGCUUC GGCACAGCACAAGCCCGCUG CG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	394
15N chemical shifts	51
1H chemical shifts	511

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (62-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	MAGNESIUM ION_7	2
9	MAGNESIUM ION_8	2
10	water_1	3
11	water_2	3
12	water_3	3
13	water_4	3
14	water_5	3
15	water_6	3
16	water_7	3
17	water_8	3
18	water_9	3
19	water_10	3
20	water_11	3
21	water_12	3
22	water_13	3

Entities:

Entity 1, RNA (62-MER) 62 residues - 20022.115 Da.

1

G

C

A

G

C

A

G

A

2

A

C

U

C

A

C

G

C

U

3

G

C

G

U

A

G

A

G

C

4

U

A

G

U

G

C

U

C

5

G

C

A

C

A

G

C

A

C

6

A

G

C

G

C

U

G

7

C

G

Entity 2, MAGNESIUM ION_1 - Mg - 24.305 Da.

1

MG

Entity 3, water_1 - 18.015 Da.

1

HOH

Samples:

J236-15N: RNA (62-MER), [U-15N], 2 mM; D2O 10%; H2O 90%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

J236-13C-15N: RNA (62-MER), [U-13C; U-15N], 2 mM; D2O 100%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

J236-ATP-13C-15N: RNA (62-MER), [U-13C; U-15N]-Ade, 2 mM; D2O 100%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

J236-CTP-13C-15N: RNA (62-MER), [U-13C; U-15N]-Cyt, 2 mM; D2O 100%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

J236-GTP-13C-15N: RNA (62-MER), [U-13C; U-15N]-Gua, 2.5 mM; D2O 100%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

J236-13C-15N-H2O: RNA (62-MER), [U-13C; U-15N], 2 mM; D2O 10%; H2O 90%; NaCacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

Sample_condition_1: pH: 6.5; pressure: 1 atm; temperature: 273 K

Sample_condition_2: pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H watergate	J236-15N	isotropic	Sample_condition_1
2D 1H-15N HSQC	J236-15N	isotropic	Sample_condition_1
2D 1H-15N HSQC NH2 only	J236-15N	isotropic	Sample_condition_1
2D HNN COSY	J236-15N	isotropic	Sample_condition_1
2D 1H-1H NOESY	J236-15N	isotropic	Sample_condition_1
2D 1H-15N CPMG-NOESY	J236-15N	isotropic	Sample_condition_1
3D 15N-edited NOESY-HSQC	J236-15N	isotropic	Sample_condition_1
3D 15N/13C-edited NOESY-HSQC	J236-13C-15N-H2O	isotropic	Sample_condition_1
2D G-specific H(NC)-TOCSY-(C)H	J236-13C-15N-H2O	isotropic	Sample_condition_1
2D A-specific H(NC)-TOCSY-(C)H	J236-13C-15N-H2O	isotropic	Sample_condition_1
2D 1H-15N MQ-(HC)N(C)H	J236-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HSQC	J236-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HMQC	J236-13C-15N	isotropic	Sample_condition_2
3D HCCH-COSY	J236-13C-15N	isotropic	Sample_condition_2
3D HCCH-TOCSY	J236-13C-15N	isotropic	Sample_condition_2
3D 13C-edited NOESY-HSQC	J236-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HSQC	J236-ATP-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HMQC	J236-ATP-13C-15N	isotropic	Sample_condition_2
3D HCCH-COSY	J236-ATP-13C-15N	isotropic	Sample_condition_2
3D HCCH-TOCSY	J236-ATP-13C-15N	isotropic	Sample_condition_2
3D 13C-edited NOESY-HSQC	J236-ATP-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HSQC	J236-CTP-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HMQC	J236-CTP-13C-15N	isotropic	Sample_condition_2
3D HCCH-COSY	J236-CTP-13C-15N	isotropic	Sample_condition_2
3D HCCH-TOCSY	J236-CTP-13C-15N	isotropic	Sample_condition_2
3D 13C-edited NOESY-HSQC	J236-CTP-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HSQC	J236-GTP-13C-15N	isotropic	Sample_condition_2
2D 1H-13C HMQC	J236-GTP-13C-15N	isotropic	Sample_condition_2
3D HCCH-COSY	J236-GTP-13C-15N	isotropic	Sample_condition_2
3D HCCH-TOCSY	J236-GTP-13C-15N	isotropic	Sample_condition_2
3D 13C-edited NOESY-HSQC	J236-GTP-13C-15N	isotropic	Sample_condition_2

Software:

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

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

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

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

NMR spectrometers:

Varian Unity 600 MHz