BMRB Entry 18656

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18656
MolProbity Validation Chart

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Title:
Major Conformation of the Internal Loop 5'GAGU/3'UGAG
Deposition date:
2012-08-12
Original release date:
2011-05-05
Authors:
Kennedy, Scott; Turner, Douglas
Citation:

Citation: Kennedy, Scott; Kierzek, Ryszard; Turner, Douglas. "Novel conformation of an RNA structural switch."  Biochemistry 51, 9257-9259 (2012).
PubMed: 23134175

Assembly members:

Assembly members:
RNA_loop, polymer, 11 residues, 3546.203 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_loop: GACGAGUGUCA

Data sets:
Data typeCount
13C chemical shifts13
15N chemical shifts5
1H chemical shifts164
31P chemical shifts10

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 11
2RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 21

Entities:

Entity 1, RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 1 11 residues - 3546.203 Da.

1   GACGAGUGUC
2   A

Samples:

sample_1: RNA_loop 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.05 mM; H2O 95%; D2O 5%

sample_2: RNA_loop 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.05 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 274 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSY 30 mssample_1isotropicsample_conditions_1
2D 1H-1H NOESY 75 mssample_1isotropicsample_conditions_1
2D 1H-1H NOESY 150 mssample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSY 14mssample_2isotropicsample_conditions_1
2D 1H-1H TOCSY 36 mssample_2isotropicsample_conditions_1
2D 1H-1H NOESY 75 mssample_2isotropicsample_conditions_1
2D 1H-1H NOESY 175 mssample_2isotropicsample_conditions_1
2D 1H-1H NOESY 400 mssample_2isotropicsample_conditions_1
2D 1H-31P HETCORsample_2isotropicsample_conditions_1

Software:

SPARKY v3.12, Goddard - chemical shift assignment, data analysis

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

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

  • Varian INOVA 600 MHz