BMRB Entry 15572

Title:
NMR STRUCTURE OF RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE   PubMed: 18399645
Deposition date:
2007-11-29
Original release date:
2008-05-29
Authors:
Popenda, Lukasz; Adamiak, Ryszard; Gdaniec, Zofia
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*CP*AP*GP*AP*AP*GP*AP*GP*CP*G)-3'), polymer, 11 residues, 3608.283 Da.
RNA_(5'-R(*CP*GP*CP*UP*CP*UP*CP*UP*GP*C)-3'), polymer, 10 residues, 3089.881 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*CP*AP*GP*AP*AP*GP*AP*GP*CP*G)-3'): GCAGAAGAGCG
RNA_(5'-R(*CP*GP*CP*UP*CP*UP*CP*UP*GP*C)-3'): CGCUCUCUGC

Data sets:
Data typeCount
13C chemical shifts112
1H chemical shifts173
31P chemical shifts19

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 11
2RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 22

Entities:

Entity 1, RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 1 11 residues - 3608.283 Da.

1   GCAGAAGAGC
2   G

Entity 2, RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 2 10 residues - 3089.881 Da.

1   CGCUCUCUGC

Samples:

sample_1: RNA (5'-R(*GP*CP*AP*GP*AP*AP*GP*AP*GP*CP*G)-3') 0.5 mM; RNA (5'-R(*CP*GP*CP*UP*CP*UP*CP*UP*GP*C)-3') 0.5 mM; D2O, [U-100% 2H], 100%; NaCl 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

sample_2: RNA (5'-R(*GP*CP*AP*GP*AP*AP*GP*AP*GP*CP*G)-3') 0.5 mM; RNA (5'-R(*CP*GP*CP*UP*CP*UP*CP*UP*GP*C)-3') 0.5 mM; D2O, [U-100% 2H], 10%; H2O 90%; NaCl 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

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: 293 K

sample_conditions_3: 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 1H-1H NOESYsample_1isotropicsample_conditions_2
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_3
1D NOEsample_2isotropicsample_conditions_3

Software:

X-PLOR NIH v2.18, C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore - refinement, structure solution

TOPSPIN v2.0, Bruker Biospin - collection, processing

FELIX v2000, Accelrys Software Inc. - chemical shift assignment, peak picking

CURVES v5.3, Lavery and Sklenar - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz