BMRB Entry 15780

Title:
NMR structure of adenosine bulged RNA duplex with C:G-A triple   PubMed: 18399645
Deposition date:
2008-05-26
Original release date:
2008-09-02
Authors:
Popenda, Lukasz; Bielecki, Lukasz; Gdaniec, Zofia; Adamiak, Ryszard
Citation:

Citation: Popenda, Lukasz; Adamiak, Ryszard; Gdaniec, Zofia. "Bulged adenosine influence on the RNA duplex conformation in solution."  Biochemistry 47, 5059-5067 (2008).

Assembly members:

Assembly members:
RNA_(5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')_, polymer, 9 residues, 2887.786 Da.
RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_, polymer, 8 residues, 2524.609 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:   Production method: chemical synthesis

Experimental 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:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')_: GUCGAGCUG
RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_: CAGCCGAC

Data sets:
Data typeCount
13C chemical shifts52
1H chemical shifts72
31P chemical shifts7

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')1
2RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')2

Entities:

Entity 1, RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3') 9 residues - 2887.786 Da.

1   GUCGAGCUG

Entity 2, RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') 8 residues - 2524.609 Da.

1   CAGCCGAC

Samples:

sample_1: RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3') 1 mM; RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') 1 mM; NaCl 50 mM; phosphate buffer 10 mM; EDTA 0.1 mM; D2O 100%

sample_2: RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3') 1 mM; RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') 1 mM; NaCl 50 mM; phosphate buffer 10 mM; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 60 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 60 mM; pH: 6.8; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-31P HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

FELIX, Accelrys Software Inc. - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection, processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CURVES, Lavery and Sklenar - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz