4HIV

Structure of actinomycin D d(ATGCGGCAT) complex

• PDB DOI:  https://doi.org/10.2210/pdb4HIV/pdb
• NAKB: 4HIV

• Classification: DNA/ANTIBIOTIC
• Organism(s): Streptomyces antibioticus
• Mutation(s): No 


• Deposited: 2012-10-12 Released: 2013-05-08 
• Deposition Author(s): Lo, Y.S., Tseng, W.H., Hou, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.260 
• R-Value Observed: 0.260 

Literature

The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.

Lo, Y.S., Tseng, W.H., Chuang, C.Y., Hou, M.H.

(2013) Nucleic Acids Res 41: 4284-4294

• PubMed: 23408860 
• DOI: https://doi.org/10.1093/nar/gkt084
• Primary Citation of Related Structures:  
  4HIV


• PubMed Abstract: 
  

The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous GpC sites separated by a single G:G mispair. To characterize the binding of ActD to CGG triplet repeat sequences, the structural basis for the strong binding of ActD to neighbouring GpC sites flanking a G:G mismatch has been determined based on the crystal structure of ActD bound to ATGCGGCAT, which contains a CGG triplet sequence. The binding of ActD molecules to GCGGC causes many unexpected conformational changes including nucleotide flipping out, a sharp bend and a left-handed twist in the DNA helix via a two site-binding model. Heat denaturation, circular dichroism and surface plasmon resonance analyses showed that adjacent GpC sequences flanking a G:G mismatch are preferred ActD-binding sites. In addition, ActD was shown to bind the hairpin conformation of (CGG)16 in a pairwise combination and with greater stability than that of other DNA intercalators. Our results provide evidence of a possible biological consequence of ActD binding to CGG triplet repeat sequences.

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Organizational Affiliation: 

Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.03 kDa 
• Atom Count: 679 
• Modelled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTINOMYCIN D	C, D	11	Streptomyces antibioticus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')	A, B	9	N/A

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	C, D	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C, D	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001	C, D	Actinomycin D	Polypeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.260 
• R-Value Observed: 0.260 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.936	α = 90
b = 86.936	β = 90
c = 49.778	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Lo, Y.S., Tseng, W.H., Hou, M.H.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references, Derived calculations, Source and taxonomy