BMRB Entry 19692

Name: NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights Into RNA-Metal Ion Interactions
Published: 2014-01-21

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PDB ID: 2mis
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19692
MolProbity Validation Chart

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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 Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights Into RNA-Metal Ion Interactions

Deposition date:

2013-12-19

Original release date:

2014-01-21

Authors:

Bonneau, Eric; Legault, Pascale

Citation:

Citation: Bonneau, Eric; Legault, Pascale. "NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights into RNA-Metal-Ion Interactions." Biochemistry 53, 579-590 (2014).
PubMed: 24364590

Assembly members:

Assembly members:
RNA_(26-MER), polymer, 26 residues, 8421.162 Da.
entity_MG, non-polymer, 24.305 Da.
entity_HOH, water, 18.015 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Host organism: Neurospora

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(26-MER): GAGCUGCAGCACGAAAGUGA CGGCUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	173
15N chemical shifts	91
1H chemical shifts	232

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (26-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	water_1	3
8	water_2	3
9	water_3	3
10	water_4	3
11	water_5	3
12	water_6	3
13	water_7	3
14	water_8	3
15	water_9	3

Entities:

Entity 1, RNA (26-MER) 26 residues - 8421.162 Da.

1

G

A

G

C

U

G

C

A

G

C

2

A

C

G

A

G

U

G

A

3

C

G

C

U

C

Entity 2, MAGNESIUM ION_1 - Mg - 24.305 Da.

1

MG

Entity 3, water_1 - 18.015 Da.

1

HOH

Samples:

sample_1: RNA (26-MER), [U-100% 15N], 1 mM; Mg2+, naturall abundance, 5 mM; KCl, naturall abundance, 50 mM

sample_2: RNA (26-MER), [U-100% 13C; U-100% 15N], 0.9 mM; Mg2+, naturall abundance, 5 mM; KCl, naturall abundance, 50 mM

sample_3: RNA (26-MER), phosphorothioate, 0.2 – 0.4 mM; Mg2+, naturall abundance, 5 mM; KCl, naturall abundance, 50 mM

sample_4: RNA (26-MER), [U-100% 13C; U-100% 15N], 0.9 mM; Mg2+, naturall abundance, 5 mM; KCl, naturall abundance, 50 mM

sample_conditions_1: ionic strength: 55 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 55 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

sample_conditions_3: ionic strength: 55 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	anisotropic	sample_conditions_2
2D 1H-15N HSQC long-range	sample_4	anisotropic	sample_conditions_1
1D 31P	sample_3	anisotropic	sample_conditions_3

Software:

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

NMRView, Johnson, One Moon Scientific - data analysis

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

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz