BMRB Entry 30283

Name: Structure and dynamics of RNA repeat expansions that cause Huntington&#039;s Disease and myotonic dystrophy type 1
Published: 2017-06-23

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PDB ID: 5vh8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30283
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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 and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1

Deposition date:

2017-04-12

Original release date:

2017-06-23

Authors:

Chen, J.; VanEtten, D.; Fountain, M.; Yildirim, I.; Disney, M.

Citation:

Citation: Chen, J.; VanEtten, D.; Fountain, M.; Yildirim, I.; Disney, M.. "Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1" Biochemistry 56, 3463-3474 (2017).
PubMed: 28617590

Assembly members:

Assembly members:
entity_1, polymer, 15 residues, 4760.849 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):
entity_1: GACCUGCUGCUGGUC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
1H chemical shifts	94

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 - 4760.849 Da.

1

G

A

C

U

G

C

U

G

C

2

U

G

U

C

Samples:

sample_1: EDTA 0.25 mM; RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), NA Adenosine, Cytidine,Guanosine, Uridine, 0.5 mM; potassium phosphate 5.0 mM

sample_2: EDTA 0.25 nM; RNA (5'-R(*GP*AP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*C)-3'), NA Adenosine, Cytidine,Guanosine, Uridine, 0.5 uM; potassium phosphate 5.0 mM

sample_conditions_2: ionic strength: 0.0112 M; pH: 6; pressure: 1 atm; temperature: 276 K

sample_conditions_1: ionic strength: 0.0112 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

AMBER v16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis, structure calculation

NMRPipe v8.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.0, Goddard - chemical shift assignment, peak picking

TOPSPIN v3.5, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance III HD UltraShield 700 MHz
Bruker Avance III HD Ascend 850 MHz