BMRB Entry 15572

Name: NMR STRUCTURE OF RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE
Published: 2008-05-29

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PDB ID: 2jxs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15572
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR STRUCTURE OF RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE

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).
PubMed: 18399645

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:

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	112
1H chemical shifts	173
31P chemical shifts	19

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 1	1
2	RNA DUPLEX CONTAINING SINGLE ADENOSINE BULGE strand 2	2

Entities:

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

1

G

C

A

G

A

G

A

G

C

2

G

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

1

C

G

C

U

C

U

C

U

G

C

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-31P HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
1D NOE	sample_2	isotropic	sample_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