BMRB Entry 36698

Name: Solution NMR structure of the 1:1 complex of NOP56 intronic G-quadruplex bound with pyridostatin
Published: 2025-12-12

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PDB ID: 9jx5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36698
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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 NMR structure of the 1:1 complex of NOP56 intronic G-quadruplex bound with pyridostatin

Deposition date:

2024-10-11

Original release date:

2025-12-12

Authors:

Yan, Z.; Wan, L.; Guo, P.; Han, D.

Citation:

Citation: Yan, Zhenzhen; He, Axin; Wan, Liqi; Gao, Qian; Jiang, Yan; Wang, Yang; Wang, Ercheng; Li, Changling; Yang, Yingquan; Li, Yingjie; Guo, Pei; Han, Da. "Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene." Adv. Sci (Weinh). 12, e2406230-e2406230 (2025).
PubMed: 40047221

Assembly members:

Assembly members:
DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), polymer, 21 residues, 6553.182 Da.
4-(2-azanylethoxy)-N2,N6-bis[4-(2-azanylethoxy)quinolin-2-yl]pyridine-2,6-dicarboxamide, non-polymer, 596.636 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(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'): GGGCCTGGGCCTGGGCCTGG G

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	136

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_7V8	2

Entities:

Entity 1, entity_1 21 residues - 6553.182 Da.

1

DG

DC

DT

DG

DC

2

DC

DT

DG

DC

DT

DG

3

DG

Entity 2, entity_7V8 - C31 H32 N8 O5 - 596.636 Da.

1

7V8

Samples:

sample_1: DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3') 0.5 mM; pyridostatin 1.5 mM; sodium phosphate 1 mM; DSS 0.02 mM; D2O, [U-2H], 99.96%

sample_2: DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3') 0.5 mM; pyridostatin 1.5 mM; sodium phosphate 1 mM; DSS 0.02 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 1 mM; pH: 7; 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_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	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