4HIV

Structure of actinomycin D d(ATGCGGCAT) complex


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 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACTINOMYCIN D
C, D
11Streptomyces antibioticusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3')
A, B
9N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MVA
Query on MVA
C, D
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
C, D
PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
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 = 86.936α = 90
b = 86.936β = 90
c = 49.778γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
  • Version 3.0: 2024-07-10
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary