BMRB Entry 30268

Name: Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop
Published: 2017-07-20

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PDB ID: 5v2r
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30268
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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:

Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop

Deposition date:

2017-03-06

Original release date:

2017-07-20

Authors:

Kauffmann, A.; Kennedy, S.; Turner, D.

Citation:

Citation: Kauffmann, Andrew; Kennedy, Scott; Zhao, Jianbo; Turner, Douglas. "Nuclear Magnetic Resonance Structure of an 8 x 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions" Biochemistry 56, 3733-3744 (2017).
PubMed: 28700212

Assembly members:

Assembly members:
RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), polymer, 15 residues, 4878.018 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 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(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'): CCAGAAACGGAUGGA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
1H chemical shifts	152
31P chemical shifts	13

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1

Entities:

Entity 1, entity_1, 1 15 residues - 4878.018 Da.

1

C

A

G

A

C

G

2

A

U

G

A

Samples:

sample_1: RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), None, 3.1 mM

sample_2: RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), None, 3.1 mM

sample_conditions_2: ionic strength: 0.1 M; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_1: ionic strength: 0.1 M; pH: 6.2; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 31P-1H COSY	sample_2	isotropic	sample_conditions_2

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis, refinement

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis

VNMR v6.1C, Varian - collection

NMR spectrometers:

Varian INOVA 600 MHz