3OMJ

Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2010-08-27 Released: 2010-09-08 
  • Deposition Author(s): Chenoweth, D.M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for cyclic py-im polyamide allosteric inhibition of nuclear receptor binding.

Chenoweth, D.M.Dervan, P.B.

(2010) J Am Chem Soc 132: 14521-14529

  • DOI: 10.1021/ja105068b
  • Primary Citation of Related Structures:  
    3OMJ

  • PubMed Abstract: 
  • Pyrrole-imidazole polyamides are a class of small molecules that can be programmed to bind a broad repertoire of DNA sequences, disrupt transcription factor-DNA interfaces, and modulate gene expression pathways in cell culture experiments. In this pa ...

    Pyrrole-imidazole polyamides are a class of small molecules that can be programmed to bind a broad repertoire of DNA sequences, disrupt transcription factor-DNA interfaces, and modulate gene expression pathways in cell culture experiments. In this paper we describe a high-resolution X-ray crystal structure of a β-amino turn-linked eight-ring cyclic Py-Im polyamide bound to the central six base pairs of the sequence d(5'-CCAGTACTGG-3')(2), revealing significant modulation of DNA shape. We compare the DNA structural perturbations induced by DNA-binding transcripton factors, androgen receptor and glucocorticoid receptor, in the major groove to those induced by cyclic polyamide binding in the minor groove. The cyclic polyamide is an allosteric modulator that perturbs the DNA structure in such a way that nuclear receptor protein binding is no longer compatible. This allosteric perturbation of the DNA helix provides a molecular basis for disruption of transcription factor-DNA interfaces by small molecules, a minimum step in chemical control of gene networks.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*(C38)P*AP*GP*TP*AP*CP*TP*GP*G)-3'A, B10N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    1P2
    Query on 1P2

    Download CCD File 
    B
    (23R,52R)-23,52-diamino-5,11,17,28,34,40,46,57-octamethyl-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46,49,54,57,60,64-icosaazanonacyclo[54.2.1.1~4,7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45,48~]hexahexaconta-1(58),4(66),6,10(65),12,16(64),18,27(63),29,33(62),35,39(61),41,45(60),47,56(59)-hexadecaene-3,9,15,21,26,32,38,44,50,55-decone
    C54 H62 N22 O10
    KELPAVUCWDTHOZ-VSGBNLITSA-N
     Ligand Interaction
    CA
    Query on CA

    Download CCD File 
    A, B
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 0.95 Å
    • R-Value Free: 0.124 
    • R-Value Work: 0.112 
    • R-Value Observed: 0.113 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 39.831α = 90
    b = 39.831β = 90
    c = 84.567γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    SHELXSphasing
    REFMACrefinement
    MOSFLMdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2010-08-27 
    • Released Date: 2010-09-08 
    • Deposition Author(s): Chenoweth, D.M.

    Revision History 

    • Version 1.0: 2010-09-08
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance