BMRB Entry 34879

Name: Solution structure of branaplam bound to the RNA duplex formed upon 5&#039;-splice site recognition
Published: 2024-02-28

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PDB ID: 8r63
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34879
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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:

Solution structure of branaplam bound to the RNA duplex formed upon 5'-splice site recognition

Deposition date:

2023-11-20

Original release date:

2024-02-28

Authors:

Malard, F.; Campagne, S.

Citation:

Citation: Malard, F.; Wolter, A.; Marquevielle, J.; Morvan, E.; Ecoutin, A.; Ruedisser, S.; Allain, F.; Campagne, S.. "The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules for rational drug design" Nucleic Acids Res. 52, 4124-4136 (2024).
PubMed: 38554107

Assembly members:

Assembly members:
entity_1, polymer, 11 residues, 3428.074 Da.
entity_2, polymer, 11 residues, 3547.162 Da.
entity_Y53, non-polymer, 393.482 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: AUACXXACCUG
entity_2: GGAGUAAGUCU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	147
1H chemical shifts	194

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	2
3	unit_3	3

Entities:

Entity 1, unit_1 11 residues - 3428.074 Da.

1

A

U

A

C

PSU

A

C

U

2

G

Entity 2, unit_2 11 residues - 3547.162 Da.

1

G

A

G

U

A

G

U

C

2

U

Entity 3, unit_3 - 393.482 Da.

1

Y53

Samples:

sample_1: RNA duplex, unit_1 0.001 M; RNA duplex, unit_2 0.001 M; Branaplam 0.001 M; MES 0.01 M; NaCl 0.05 M

sample_conditions_1: ionic strength: 50 mM; pH: 5.5; pressure: 1 atm; temperature: 293 K

Experiments:

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

Software:

AmberTools v2023, Case D - refinement

CYANA v3, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking

NMR spectrometers:

Bruker AVANCE III HD 900 MHz