Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.75 kDa 
• Atom Count: 315 
• Modelled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 6J0H

Crystal structure of Actinomycin D- d(TTGGCGAA) complex

• PDB DOI: 10.2210/pdb6J0H/pdb
• NDB: 6J0H

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


• Deposited: 2018-12-24 Released: 2019-07-24 
• Deposition Author(s): Satange, R.B., Hou, M.H.

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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 

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

• PubMed: 31361900 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinomycin D	B	11	Streptomyces sp.	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*GP*GP*CP*GP*AP*A)-3')	A	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	B	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	B	Actinomycin D	Polypeptide / 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 = 59.5	α = 90
b = 59.5	β = 90
c = 93.489	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Satange, R.B., Hou, M.H.

Revision History  

• 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