BMRB Entry 15781

Name: NMR structure of uridine bulged RNA duplex
Published: 2008-09-02

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PDB ID: 2k41
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15781
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of uridine bulged RNA duplex

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).
PubMed: 18399645

Assembly members:

Assembly members:
RNA_(5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3'), polymer, 9 residues, 2864.746 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:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	110
1H chemical shifts	148
31P chemical shifts	15

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	1
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	2

Entities:

Entity 1, RNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3') 9 residues - 2864.746 Da.

1

G

U

C

G

U

G

C

U

G

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

1

C

A

G

C

G

A

C

Samples:

sample_1: RNA (5'-R(*GP*UP*CP*GP*UP*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*UP*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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
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_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