BMRB Entry 30547

Name: RNA Duplex containing the internal loop 5&#039;-GCAU/3&#039;-UACG
Published: 2019-02-08

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PDB ID: 6n8h
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30547
MolProbity Validation Chart

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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:

RNA Duplex containing the internal loop 5'-GCAU/3'-UACG

Deposition date:

2018-11-29

Original release date:

2019-02-08

Authors:

Berger, K.; Kennedy, S.; Turner, D.

Citation:

Citation: Berger, K.; Kennedy, S.; Turner, D.. "Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures" Biochemistry 58, 1094-1108 (2019).
PubMed: 30702283

Assembly members:

Assembly members:
RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3'), polymer, 10 residues, 3191.964 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32644 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*GP*GP*GP*CP*AP*UP*CP*CP*G)-3'): CGGGCAUCCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	18
1H chemical shifts	88
31P chemical shifts	5

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 10 residues - 3191.964 Da.

1

C

G

C

A

U

C

G

Samples:

sample_1: RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3'), none, 1 mM; sodium chloride 80 mM; sodium phosphate 50 mM

sample_conditions_1: ionic strength: 130 mM; pH: 6.2; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
HETCOR	sample_1	isotropic	sample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment, data analysis

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

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

NMR spectrometers:

Varian INOVA 600 MHz