BMRB Entry 17401

Name: NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
Published: 2011-02-04

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PDB ID: 2l8u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17401
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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:

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1

Deposition date:

2011-01-07

Original release date:

2011-02-04

Authors:

Parkesh, Raman; Fountain, Matthew; Disney, Matthew

Citation:

Citation: Parkesh, Raman; Fountain, Matthew; Disney, Matthew. "NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)(2) Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1." Biochemistry 50, 599-601 (2011).
PubMed: 21204525

Assembly members:

Assembly members:
RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_, polymer, 9 residues, 2862.776 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_: CCGCUGCGG

Data sets:

assigned_chemical_shifts
- r(CCGCUGCGG)

Data type	Count
1H chemical shifts	47

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(CPCPGPCPUPGPCPGP*G)-3')_1	1
2	RNA (5'-R(CPCPGPCPUPGPCPGP*G)-3')_2	1

Entities:

Entity 1, RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')_1 9 residues - 2862.776 Da.

1

C

G

C

U

G

C

G

Samples:

rCCGCUGCGG: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3') 1.5 ± 0.1 mM; sodium chloride 100 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.2; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	rCCGCUGCGG	isotropic	sample_conditions_1
2D 1H-1H NOESY	rCCGCUGCGG	isotropic	sample_conditions_1
2D 1H-1H TOCSY	rCCGCUGCGG	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - geometry optimization

SPARKY v3.111, Goddard - chemical shift assignment, data analysis, peak picking

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

NMR spectrometers:

Varian INOVA 500 MHz