1UNM

Crystal structure of 7-Aminoactinomycin D with non-complementary DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)

Alexopoulos, E.C.Jares-Erijman, E.A.Jovin, T.M.Klement, R.Machinek, R.Sheldrick, G.M.Uson, I.

(2005) Acta Crystallogr.,Sect.D 61: 407

  • DOI: 10.1107/S090744490500082X
  • Primary Citation of Related Structures:  1UNJ

  • PubMed Abstract: 
  • The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG ...

    The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG[Br(5)U]T-3' provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A*T)*T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.


    Organizational Affiliation

    Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
7-AMINOACTINOMYCIN D
E, F
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*AP*GP*BRU*TP)-3'A,B,C,D6N/A
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000010
Query on PRD_000010
E,F7-AminoActinomycinPolypeptide / Antibiotic

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A, B, C, D
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 51.586α = 90.00
b = 70.975β = 90.00
c = 39.453γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXDphasing
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2011-07-20
    Type: Other, Structure summary
  • Version 1.3: 2012-11-30
    Type: Other