3KUY

DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent

Davey, G.E.Wu, B.Dong, Y.Surana, U.Davey, C.A.

(2010) Nucleic Acids Res 38: 2081-2088

  • DOI: 10.1093/nar/gkp1174
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DNA stretching in the nucleosome core can cause dramatic structural distortions, which may influence compaction and factor recognition in chromatin. We find that the base pair unstacking arising from stretching-induced extreme minor groove kinking ne ...

    DNA stretching in the nucleosome core can cause dramatic structural distortions, which may influence compaction and factor recognition in chromatin. We find that the base pair unstacking arising from stretching-induced extreme minor groove kinking near the nucleosome centre creates a hot spot for intercalation and alkylation by a novel anticancer compound. This may have far reaching implications for how chromatin structure can influence binding of intercalator species and indicates potential for the development of site selective DNA-binding agents that target unique conformational features of the nucleosome.


    Organizational Affiliation

    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
119Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
125Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATV
Query on ATV

Download CCD File 
I, J
2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione
C15 H11 N O3
TVMJTOKZNPCXOO-SNVBAGLBSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.161α = 90
b = 109.588β = 90
c = 182.413γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-11-28 
  • Released Date: 2010-01-05 
  • Deposition Author(s): Wu, B., Davey, C.A.

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance