BMRB Entry 25291

Name: RNA duplex
Published: 2015-09-28

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PDB ID: 2mvy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25291
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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

Deposition date:

2014-10-20

Original release date:

2015-09-28

Authors:

Lynch, Stephen; Kool, Eric

Citation:

Citation: Roost, Caroline; Lynch, Stephen; Batista, Pedro; Qu, Kun; Chang, Howard; Kool, Eric. "Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification" J. Am. Chem. Soc. 137, 2107-2115 (2015).
PubMed: 25611135

Assembly members:

Assembly members:
RNA, polymer, 10 residues, Formula weight is not available

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: GGACUAGUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	48
1H chemical shifts	77
31P chemical shifts	8

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA, chain 1	1
2	RNA, chain 2	1

Entities:

Entity 1, RNA, chain 1 10 residues - Formula weight is not available

1

G

A

C

U

A

G

U

C

Samples:

sample_1: RNA 0.2 mM; sodium chloride 100 mM; EDTA 0.1 mM; sodium phosphate 10 mM

sample_2: RNA 0.2 mM; sodium chloride 100 mM; EDTA 0.1 mM; sodium phosphate 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

VNMR v6.1C, Varian - collection, processing

SPARKY v3.115, Goddard - chemical shift assignment, data analysis

X-PLOR_NIH v2.36, Brunger - structure solution

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 500 MHz