BMRB Entry 50637

Name: Minimal trans VS ribozyme in 5 mM MgCl2
Published: 2021-10-06

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50637

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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:

Minimal trans VS ribozyme in 5 mM MgCl2

Deposition date:

2020-12-11

Original release date:

2021-10-06

Authors:

Dagenais, Pierre; Desjardins, Genevieve; Legault, Pascale

Citation:

Citation: Dagenais, Pierre; Desjardins, Genevieve; Legault, Pascale. "An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme" Nucleic Acids Res. 49, 11959-11973 (2021).
PubMed: 34718697

Assembly members:

Assembly members:
entity_1, polymer, 101 residues, 32652.55626 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: recombinant technology Host organism: Synthetic Vector: pTZ19R-derived plasmid

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GCAGGGAACUCACCUCCCCU UGGGUCGUAGCAGUUGACUA CUGUUAUGUGAUUGGUAGAG GCUAAGUGACGCCGUAAGGC GCAGCACAGCACAAGCCCGC G

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
spectral_peak_list

Data type	Count
15N chemical shifts	78
1H chemical shifts	78

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Minimal trans VS ribozyme	1

Entities:

Entity 1, Minimal trans VS ribozyme 101 residues - 32652.55626 Da.

1

G

C

A

G

A

C

U

2

C

A

C

U

C

U

3

U

G

U

C

G

U

A

G

4

C

A

G

U

G

A

C

U

A

5

C

U

G

U

A

U

G

U

G

6

A

U

G

U

A

G

A

G

7

G

C

U

A

G

U

G

A

C

8

G

C

G

U

A

G

C

9

G

C

A

G

C

A

C

A

G

C

10

A

C

A

G

C

G

C

11

G

Samples:

sample_1: TR4P, [U-15N], 1.7 mM; Na cacodylate 10 mM; KCl 50 mM; MgCl2 5 mM; NaN3 0.05 mM

sample_conditions_1: pH: 6.500; pressure: 1.000 atm; temperature: 288.000 K

sample_conditions_2: pH: 6.500; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC/HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC/HMQC	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2

Software:

CcpNmr Analysis v2.5 - Chemical shift assignments, data analysis

NMRPipe v9.7 - Data processing, data analysis

NMR spectrometers:

Bruker Avance 700 MHz