BMRB Entry 36612

Name: NMR structure of a bimolecular parallel G-quadruplex formed by AAGGG repeats from pathogenic RFC1 gene
Published: 2025-12-12

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PDB ID: 8x1v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36612
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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 structure of a bimolecular parallel G-quadruplex formed by AAGGG repeats from pathogenic RFC1 gene

Deposition date:

2023-11-08

Original release date:

2025-12-12

Authors:

Wang, Y.; Guo, P.; Han, D.

Citation:

Citation: Wang, Yang; Wang, Junyan; Yan, Zhenzhen; Hou, Jianing; Wan, Liqi; Yang, Yingquan; Liu, Yu; Yi, Jie; Guo, Pei; Han, Da. "Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS." Nucleic Acids Res. 52, 2698-2710 (2024).
PubMed: 38266156

Assembly members:

Assembly members:
DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), polymer, 24 residues, 3809.518 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 Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'): AAGGGAAGGGAA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	196

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 24 residues - 3809.518 Da.

1

DA

DG

DA

DG

2

DA

Samples:

sample_1: DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3') 0.9 mM; potassium chloride 150 mM; sodium phosphate 1 mM; D2O, [U-2H], 99.96%

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; 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 COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMBC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - chemical shift assignment

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

NMR spectrometers:

Bruker AVANCE 600 MHz