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PDB ID: 9jo1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36695
MolProbity Validation Chart

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All files associated with the entry

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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Name: NMR Solution structure of the 2:1 Berberine-BLM-G4 Complex
Published: 2026-06-08

Title:

NMR Solution structure of the 2:1 Berberine-BLM-G4 Complex

Deposition date:

2024-09-24

Original release date:

2026-06-08

Authors:

Wang, K.

Citation:

Citation: Wang, Y.; Bian, Y.; Chen, X.; Li, J.; Liu, Y.; Kong, L.; Wang, K.. "BLM G-quadruplex stabilizers synergize with PARP inhibitor to kill BRCA wild-type colon cancer cells" .

Assembly members:

Assembly members:
DNA (5'-D(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T*)-3'), polymer, 21 residues, 6698.32 Da.
BERBERINE, non-polymer, 336.361 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(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T*)-3'): TGAGGGAGGGCGGGAGGGAA T

Data sets:

assigned_chemical_shifts
- starch_output

Data type	Count
1H chemical shifts	228

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_BER_1	2
3	entity_BER_2	2

Entities:

Entity 1, entity_1 21 residues - 6698.32 Da.

1

DT

DG

DA

DG

DA

DG

2

DC

DG

DA

DG

DA

3

DT

Entity 2, entity_BER_1 - C20 H18 N O4 - 336.361 Da.

1

BER

Samples:

sample_1: BLM_Pu21T_BER 1.93 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 288 K

sample_conditions_2: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
2D DQF-COSY	sample_1	isotropic	sample_conditions_2

Software:

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

TopSpin, Bruker Biospin - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMRFAM-SPARKY, Woonghee Lee - peak picking

NMR spectrometers:

Bruker AVANCE II 600 MHz

BMRB Entry 36695