BMRB Entry 25654

Title:
NMR structure of the II-III-VI three-way junction from the VS ribozyme
Deposition date:
2015-06-09
Original release date:
2015-07-03
Authors:
Bonneau, Eric; Girard, Nicolas; Lemieux, Sebastien; Legault, Pascale
Citation:

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).
PubMed: 26124200

Assembly members:

Assembly members:
RNA_(62-MER), polymer, 62 residues, 20022.115 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pTZ19R-derived pTR-4

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts394
15N chemical shifts51
1H chemical shifts511

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (62-MER)1

Entities:

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

1   GCAGCAGGGA
2   ACUCACGCUU
3   GCGUAGAGGC
4   UAAGUGCUUC
5   GGCACAGCAC
6   AAGCCCGCUG
7   CG

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:

NameSampleSample stateSample conditions
1D 1H watergateJ236-15NisotropicSample_condition_1
2D 1H-15N HSQCJ236-15NisotropicSample_condition_1
2D 1H-15N HSQC NH2 onlyJ236-15NisotropicSample_condition_1
2D HNN COSYJ236-15NisotropicSample_condition_1
2D 1H-1H NOESYJ236-15NisotropicSample_condition_1
2D 1H-15N CPMG-NOESYJ236-15NisotropicSample_condition_1
3D 15N-edited NOESY-HSQCJ236-15NisotropicSample_condition_1
3D 15N/13C-edited NOESY-HSQCJ236-13C-15N-H2OisotropicSample_condition_1
2D G-specific H(NC)-TOCSY-(C)HJ236-13C-15N-H2OisotropicSample_condition_1
2D A-specific H(NC)-TOCSY-(C)HJ236-13C-15N-H2OisotropicSample_condition_1
2D 1H-15N MQ-(HC)N(C)HJ236-13C-15NisotropicSample_condition_2
2D 1H-13C HSQCJ236-13C-15NisotropicSample_condition_2
2D 1H-13C HMQCJ236-13C-15NisotropicSample_condition_2
3D HCCH-COSYJ236-13C-15NisotropicSample_condition_2
3D HCCH-TOCSYJ236-13C-15NisotropicSample_condition_2
3D 13C-edited NOESY-HSQCJ236-13C-15NisotropicSample_condition_2
2D 1H-13C HSQCJ236-ATP-13C-15NisotropicSample_condition_2
2D 1H-13C HMQCJ236-ATP-13C-15NisotropicSample_condition_2
3D HCCH-COSYJ236-ATP-13C-15NisotropicSample_condition_2
3D HCCH-TOCSYJ236-ATP-13C-15NisotropicSample_condition_2
3D 13C-edited NOESY-HSQCJ236-ATP-13C-15NisotropicSample_condition_2
2D 1H-13C HSQCJ236-CTP-13C-15NisotropicSample_condition_2
2D 1H-13C HMQCJ236-CTP-13C-15NisotropicSample_condition_2
3D HCCH-COSYJ236-CTP-13C-15NisotropicSample_condition_2
3D HCCH-TOCSYJ236-CTP-13C-15NisotropicSample_condition_2
3D 13C-edited NOESY-HSQCJ236-CTP-13C-15NisotropicSample_condition_2
2D 1H-13C HSQCJ236-GTP-13C-15NisotropicSample_condition_2
2D 1H-13C HMQCJ236-GTP-13C-15NisotropicSample_condition_2
3D HCCH-COSYJ236-GTP-13C-15NisotropicSample_condition_2
3D HCCH-TOCSYJ236-GTP-13C-15NisotropicSample_condition_2
3D 13C-edited NOESY-HSQCJ236-GTP-13C-15NisotropicSample_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