BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34265

Title: Solution structure of the r(UGGUGGU)4 RNA quadruplex   PubMed: 30341177

Authors: Andralojc, W.; Gdaniec, Z.

Citation: Andralojc, W.; Malgowska, M.; Sarzynska, J.; Pasternak, K.; Szpotkowski, K.; Kierzek, R.; Gdaniec, Z.. "Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus."  RNA 25, 121-134 (2019).

Assembly members:
entity_1, polymer, 7 residues, 2254.363 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):
entity_1: UGGUGGU

Data typeCount
13C chemical shifts44
1H chemical shifts169
31P chemical shifts7

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_1, 31
4entity_1, 41

Entities:

Entity 1, entity_1, 1 7 residues - 2254.363 Da.

1   UGGUGGU

Samples:

sample_1: pUGGUGGU 2.0 mM; phosphate buffer 10 mM; potassium chloride 50 mM

sample_2: pUGGUGGU 2.0 mM; phosphate buffer 10 mM; potassium chloride 0.05 mM

sample_conditions_1: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 0.06 M; pH: 6.8; pressure: 1 bar; temperature: 333 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_1isotropicsample_conditions_3
2D 1H-31P COSYsample_1isotropicsample_conditions_3

Software:

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

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AvanceIII 700 MHz

Related Database Links: