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 34324

Title: Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context)   PubMed: 31700156

Authors: Deb, I.; Popenda, L.; Sarzynska, J.; Gdaniec, Z.

Citation: Deb, I.; Popenda, L.; Sarzynska, J.; Malgowska, M.; Lahiri, A.; Gdaniec, Z.; Kierzek, R.. "Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair."  Sci. Rep. 9, 16278-16278 (2019).

Assembly members:
entity_1, polymer, 9 residues, 2832.727 Da.
entity_2, polymer, 9 residues, 2855.767 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: UCAGXCAGU
entity_2: ACUGACUGA

Data sets:
Data typeCount
13C chemical shifts83
1H chemical shifts155
31P chemical shifts16

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 9 residues - 2832.727 Da.

1   UCAGPSUCAGU

Entity 2, entity_2 9 residues - 2855.767 Da.

1   ACUGACUGA

Samples:

sample_1: pUCAG(PSU)CAGU 0.5 mM; pACUGACUGA 0.5 mM; sodium phosphate 10 mM; sodium chloride 150 mM; EDTA 0.1 mM

sample_2: pUCAG(PSU)CAGU 0.5 mM; pACUGACUGA 0.5 mM; sodium phosphate 10 mM; sodium chloride 150 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_3
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-31P COSYsample_1isotropicsample_conditions_1
2D 1H-31P hetero TOCSY-NOESYsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

Felix, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

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

NMR spectrometers:

  • Bruker AVANCE III 700 MHz

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