9JL7 | pdb_00009jl7

Crystal structure of Actinomycin D-Doxorubicin-d(AGCCGT)2 DNA ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9JL7/pdb
• NAKB: 9JL7

• Classification: DNA/ANTIBIOTIC
• Organism(s): synthetic construct, Streptomyces parvulus
• Mutation(s): No 


• Deposited: 2024-09-18 Released: 2025-03-12 
• Deposition Author(s): Li, H.J., Satange, R.B., Hou, M.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis.

Chang, C.C., Li, H.J., Satange, R., Lin, S.M., Chen, T.L., Lin, C.C., Neidle, S., Hou, M.H.

(2025) J Med Chem 68: 6601-6615

• PubMed: 40032551 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c03203
• Primary Citation Related Structures: 
  9JL7


• PubMed Abstract: 
  

  Chemotherapeutic drugs are commonly used to treat cancers lacking targeted therapy options. However, their low specificity limits their treatment effectiveness. We report here that the cooperative binding of doxorubicin (Dox) with actinomycin D (ActD) enhances the specificity for consecutive GCCG sites in DNA. Using X-ray crystallography, we determined the crystal structure of ActD and Dox bound to d(AGCCGT) ₂ DNA. ActD intercalation at the GpC site induces a novel Dox binding mode at the adjacent CpG step. This ensures a snug fit, avoids steric clashes, and enhances the specificity. Transcriptome analysis revealed that combining Dox with ActD synergistically down-regulates EGFR in TNBC cells. Additionally, it reduces EGFR promoter activity. In vivo, the combination significantly suppresses tumor growth and outperforms the standard Dox and cyclophosphamide regimen in inhibiting metastasis. This study highlights targeting the activated EGFR pathway with sequence-specific DNA-targeting drug combinations as a potential TNBC treatment.

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Organizational Affiliation: 
• Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
Post Baccalaureate Medicine, School of Medicine, National Chung Hsing University, Taichung 402, Taiwan.
Institute of Biomedical Science, National Chung Hsing University, Taichung 402, Taiwan.
The School of Pharmacy, University College London, London WC1N 1AX, U.K.
Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.65 kDa 
• Atom Count: 469 
• Modeled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinomycin D	C [auth G]	11	Streptomyces parvulus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*CP*GP*T)-3')	A	6	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*GP*CP*T)-3')	B	6	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM2 (Subject of Investigation/LOI)	D [auth A]	DOXORUBICIN C27 H29 N O11 AOJJSUZBOXZQNB-TZSSRYMLSA-N
MN	E [auth A], F [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DVA	C [auth G]	D-PEPTIDE LINKING	C5 H11 N O2		--
MVA	C [auth G]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C [auth G]	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001	C [auth G]	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.002	α = 90
b = 27.002	β = 90
c = 205.993	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Li, H.J., Satange, R.B., Hou, M.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2628-M-005-001-MY4

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references