BMRB Entry 19662

Name: NMR structure of the I-V kissing-loop interaction of the Neurospora VS ribozyme
Published: 2014-01-10

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PDB ID: 2mi0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19662
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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 I-V kissing-loop interaction of the Neurospora VS ribozyme

Deposition date:

2013-12-05

Original release date:

2014-01-10

Authors:

Bouchard, Patricia; Legault, Pascale

Citation:

Citation: Bouchard, Patricia; Legault, Pascale. "Structural insights into substrate recognition by the neurospora varkud satellite ribozyme: importance of u-turns at the kissing-loop junction." Biochemistry 53, 258-269 (2014).
PubMed: 24325625

Assembly members:

Assembly members:
RNA_(5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), polymer, 22 residues, 7049.290 Da.
RNA_(5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), polymer, 21 residues, 6721.066 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'): GAGCAGCAUCGUCGGCUGCU CA
RNA_(5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'): GCGGCAGUUGACUACUGUCG C

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	186
15N chemical shifts	67
1H chemical shifts	231

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	1
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	2

Entities:

Entity 1, RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3') 22 residues - 7049.290 Da.

1

G

A

G

C

A

G

C

A

U

C

2

G

U

C

G

C

U

G

C

U

3

C

A

Entity 2, RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 21 residues - 6721.066 Da.

1

G

C

G

C

A

G

U

G

2

A

C

U

A

C

U

G

U

C

G

3

C

Samples:

sample_1: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3')1.3 – 2.2 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), [U-15N], 1.3 – 2.2 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_2: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3') 1.5 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), [U-13C; U-15N], 1.5 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_3: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-15N], 1.4 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.4 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_4: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-13C; U-15N], 1.7 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.7 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_5: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-13C; U-15N]-Gua, 1.4 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.4 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_6: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-13C; U-15N]-Gua, 1.4 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.4 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_7: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-15N], 1.4 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.4 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_8: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3') 1.3 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), [U-15N], 1.3 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_9: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-13C; U-15N], 1.7 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') 1.7 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_10: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3') 1.5 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), [U-13C; U-15N], 1.5 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM

sample_11: RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'), [U-15N], 0.2 – 0.3 mM; RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), [U-15N], 0.2 – 0.3 mM; TRIS, [U-2H], 10 mM; sodium chloride 50 mM; sodium azide 0.05 mM; magnesium chloride 5 mM; Pf1 phage 14.6-20.5 mg/mL

sample_conditions_1: ionic strength: 55 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 55 mM; pH: 7.0; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_3	isotropic	sample_conditions_1
2D 1H-15N NHH COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N NHH COSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HMQC J=21Hz	sample_7	isotropic	sample_conditions_1
2D 1H-15N HMQC J=21Hz	sample_8	isotropic	sample_conditions_1
2D 1H-15N CPMG NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-15N CPMG NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-1H flip-back watergate NOESY	sample_3	isotropic	sample_conditions_1
3D 15N-edited NOESY-HSQC	sample_1	isotropic	sample_conditions_1
3D 15N-edited NOESY-HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	sample_6	isotropic	sample_conditions_1
3D 15N/13C-edited NOESY-HSQC	sample_9	isotropic	sample_conditions_1
3D 15N/13C-edited NOESY-HSQC	sample_10	isotropic	sample_conditions_1
3D 13C-edited HMQC-NOESY	sample_2	isotropic	sample_conditions_1
3D 13C-edited HMQC-NOESY	sample_4	isotropic	sample_conditions_1
3D 13C-edited HMQC-NOESY	sample_5	isotropic	sample_conditions_1
3D 13C-edited HMQC-NOESY	sample_6	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_4	isotropic	sample_conditions_1
3D HCCH-COSY	sample_6	isotropic	sample_conditions_1
1D 15N-decoupled 1H watergate	sample_1	isotropic	sample_conditions_1
1D 15N-decoupled 1H watergate	sample_3	isotropic	sample_conditions_1
1D 15N-filtered 1H watergate	sample_1	isotropic	sample_conditions_1
1D 15N-filtered 1H watergate	sample_3	isotropic	sample_conditions_1
1D 15N-edited 1H watergate	sample_1	isotropic	sample_conditions_1
1D 15N-edited 1H watergate	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_11	anisotropic	sample_conditions_1

Software:

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

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

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

PyMOL, Schrodinger - Structure analysis, Structure display

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

CURVES_+, (CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K. - Structure analysis

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz