6J0H

Crystal structure of Actinomycin D- d(TTGGCGAA) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.

Satange, R.Chuang, C.Y.Neidle, S.Hou, M.H.

(2019) Nucleic Acids Res 47: 8899-8912

  • DOI: 10.1093/nar/gkz653
  • Primary Citation of Related Structures:  
    6J0H, 6J0I

  • PubMed Abstract: 
  • DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism ...

    DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.


    Organizational Affiliation

    Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actinomycin DB11Streptomyces sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')A8synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA
B L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
B PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000001
Query on PRD_000001
BActinomycin DPolypeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.5α = 90
b = 59.5β = 90
c = 93.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-09
    Changes: Database references, Derived calculations