BMRB Entry 17292

Name: NMR structure of the A730 loop of the Neurospora VS ribozyme
Published: 2011-01-27

Click here to enlarge.

PDB ID: 2l5z
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17292
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

NMR structure of the A730 loop of the Neurospora VS ribozyme

Deposition date:

2010-11-11

Original release date:

2011-01-27

Authors:

Desjardins, Genevieve; Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jerome; Legault, Pascale

Citation:

Citation: Desjardins, Genevieve; Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jerome; Legault, Pascale. "NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site." Nucleic Acids Res. 39, 4427-4437 (2011).
PubMed: 21266483

Assembly members:

Assembly members:
VS_ribozyme_SVI_RNA_(26-MER), polymer, 26 residues, 8421.162 Da.

Natural source:

Natural source: Common Name: Neurospora Taxonomy ID: 5140 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Neurospora not available

Experimental source:

Experimental source: Production method: enzymatic synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VS_ribozyme_SVI_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
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (26-MER)	1

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

Samples:

sample_1: VS ribozyme SVI RNA (26-MER)0.4 – 1.8 mM; H2O 90%; D2O 10%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_2: VS ribozyme SVI RNA (26-MER)0.4 – 1.8 mM; D2O 100%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_3: VS ribozyme SVI RNA (26-MER), [U-15N], 0.4 – 1.8 mM; H2O 90%; D2O 10%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_4: VS ribozyme SVI RNA (26-MER), [U-15N], 0.4 – 1.8 mM; D2O 100%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_5: VS ribozyme SVI RNA (26-MER), [U-13C; U-15N], 0.4 – 1.8 mM; H2O 90%; D2O 10%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_6: VS ribozyme SVI RNA (26-MER), [U-13C; U-15N], 0.4 – 1.8 mM; D2O 100%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM

sample_7: VS ribozyme SVI RNA (26-MER), [U-15N], 0.4 ± 0.1 mM; H2O 90%; D2O 10%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM; Pf1 filamentous phage 17 mg/mL

sample_8: VS ribozyme SVI RNA (26-MER), [U-13C; U-15N], 0.4 ± 0.1 mM; D2O 100%; sodium cacodylate 10 mM; KCl 50 mM; NaN3 0.05 mM; MgCl2 5 mM; Pf1 filamentous phage 17 mg/mL

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

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C CT-HSQC	sample_6	isotropic	sample_conditions_2
2D 1H-13C HMQC	sample_6	isotropic	sample_conditions_2
2D 1H-15N MQ-(HC)N(C)H	sample_6	isotropic	sample_conditions_2
3D CT-HCCH-COSY	sample_6	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
3D 13C-edited HMQC-NOESY	sample_6	isotropic	sample_conditions_2
1D flip-back watergate 1H	sample_1	isotropic	sample_conditions_1
2D flip-back watergate NOESY	sample_1	isotropic	sample_conditions_1
2D imino- and amino-optimized 2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D H(NCCC)H for uracil and cytosine residues	sample_5	isotropic	sample_conditions_1
2D H(NC)-TOCSY-(C)H for guanosine residues	sample_5	isotropic	sample_conditions_1
2D (H)N(C)-TOCSY-(C)H for adenosine residues	sample_5	isotropic	sample_conditions_1
2D 1H-15N CPMG-NOESY	sample_3	isotropic	sample_conditions_1
2D 1H 15N HMQC optimized for transfers via J=7.0 Hz and J=21 Hz	sample_4	isotropic	sample_conditions_2
2D HNN-COSY	sample_3	isotropic	sample_conditions_1
2D DQF COSY	sample_2	isotropic	sample_conditions_2
3D HCCH-E.COSY	sample_6	isotropic	sample_conditions_2
2D imino-optimized 2D 1H-15N HSQC	sample_7	anisotropic	sample_conditions_1
Spin-state selective experiments	sample_8	isotropic	sample_conditions_2
Spin-state selective experiments	sample_6	anisotropic	sample_conditions_2

Software:

Module v1.0, (Module) - data analysis

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

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

PyMol, PyMol (Schr dinger) - structure analysis, structure display

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Varian INOVA 800 MHz