BMRB Entry 31190

Name: Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1
Published: 2024-08-02

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PDB ID: 9cpi
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31190
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:

Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1

Deposition date:

2024-07-18

Original release date:

2024-08-02

Authors:

Chen, J.; Taghavi, A.; Disney, M.; Fountain, M.; Childs-Disney, J.

Citation:

Citation: Chen, J.; Taghavi, A.; Frank, A.; Fountain, M.; Choudhary, S.; Roy, S.; Childs-Disney, J.; Disney, M.. "Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1." Bioorg. Med. Chem. Lett. 111, 129888-129888 (2024).
PubMed: 39002937

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, 4133.501 Da.
entity_2, non-polymer, 376.455 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: GACAGCUGCUGUC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	78

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	2

Entities:

Entity 1, unit_1 13 residues - 4133.501 Da.

1

G

A

C

A

G

C

U

G

C

U

2

G

U

C

Entity 2, unit_3 - C21 H24 N6 O - 376.455 Da.

1

A1AZL

Samples:

sample_1: RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3') 0.3 mM; 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium 0.6 mM; potassium phosphate 5 mM; EDTA 0.25 mM

sample_2: RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3') 0.3 mM; 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium 0.6 mM; potassium phosphate 5 mM; EDTA 0.25 mM

sample_conditions_1: ionic strength: 5 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.0; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 5 mM; pH: 6.0; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2
2D NOESY	sample_2	isotropic	sample_conditions_3

Software:

TopSpin v3.5, Bruker Biospin - processing

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

NMRFAM-SPARKY v1.3, NMRFAM-SPARKY - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III HD 700 MHz
Bruker AVANCE III HD 850 MHz