BMRB Entry 15538

Name: Structure of a high affinity anti-NFkB RNA aptamer
Published: 2007-12-18

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PDB ID: 2jwv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15538
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of a high affinity anti-NFkB RNA aptamer

Deposition date:

2007-10-25

Original release date:

2007-12-18

Authors:

Reiter, Nicholas; Maher, L. James; Butcher, Samuel

Citation:

Citation: Reiter, Nicholas; Maher, L. James; Butcher, Samuel. "DNA mimicry by a high affinity anti-NF-kB RNA apatamer" Nucleic Acids Res. 36, 1227-1236 (2008).
PubMed: 18160411

Assembly members:

Assembly members:
RNA, polymer, 29 residues, 132.116 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: recombinant technology Host organism: not applicable Vector: T7 RNA polymerase

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA: GAUACUUGAAACUGUAAGGU UGGCGUAUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	193
15N chemical shifts	31
1H chemical shifts	256

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1

Entities:

Entity 1, RNA 29 residues - 132.116 Da.

1

G

A

U

A

C

U

G

A

2

A

C

U

G

U

A

G

U

3

U

G

C

G

U

A

U

C

Samples:

sample_1: RNA, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; KCl 50 mM; H20 90%; D2O 10%

Sample_D2O: RNA 1 ± 0.2 mM; D2O 100%

sample_conditions_1: ionic strength: 0.05 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	Sample_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	Sample_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

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

NMR spectrometers:

Varian INOVA 900 MHz
Bruker DMX 750 MHz