BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 30268

Title: Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop   PubMed: 28700212

Authors: Kauffmann, A.; Kennedy, S.; Turner, D.

Citation: Kauffmann, Andrew; Kennedy, Scott; Zhao, Jianbo; Turner, Douglas. "Nuclear Magnetic Resonance Structure of an 8 x 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions"  Biochemistry 56, 3733-3744 (2017).

Assembly members:
RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), polymer, 15 residues, 4878.018 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'): CCAGAAACGGAUGGA

Data sets:
Data typeCount
1H chemical shifts152
31P chemical shifts13

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21

Entities:

Entity 1, entity_1, 1 15 residues - 4878.018 Da.

1   CCAGAAACGG
2   AUGGA

Samples:

sample_1: RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), None, 3.1 mM

sample_2: RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), None, 3.1 mM

sample_conditions_2: ionic strength: 0.1 M; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_1: ionic strength: 0.1 M; pH: 6.2; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 31P-1H COSYsample_2isotropicsample_conditions_2

Software:

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

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis, refinement

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

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

SPARKY, Goddard - chemical shift assignment, data analysis

VNMR v6.1C, Varian - collection

NMR spectrometers:

  • Varian INOVA 600 MHz

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