1N4B

Solution Structure of the undecamer CGAAAC*TTTCG


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: the structure submitted is the lowest energy structure of a an ensemble of selected ten structures 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution Structure of a DNA Duplex Containing Mispair-Aligned N4C-Ethyl-N4C Interstrand Cross-Linked Cytosines

Webba da Silva, M.Noronha, A.M.Noll, D.M.Miller, P.S.Colvin, O.M.Gamcsik, M.P.

(2002) Biochemistry 41: 15181-15188


  • PubMed Abstract: 
  • The solution structure of an interstrand cross-linked self-complementary oligodeoxynucleotide containing directly opposed alkylated N(4)C-ethyl-N(4)C cytosine bases was determined by molecular dynamics calculations guided by NMR-derived restraints. T ...

    The solution structure of an interstrand cross-linked self-complementary oligodeoxynucleotide containing directly opposed alkylated N(4)C-ethyl-N(4)C cytosine bases was determined by molecular dynamics calculations guided by NMR-derived restraints. The undecamer d(CGAAACTTTCG)(2), where C represents directly opposed alkylated N(4)C-ethyl-N(4)C cytosine bases, serves as model for the cytotoxic cross-links formed by bifunctional alkylating agents used in cancer therapy. The structure of the duplex shows the cross-link protruding into the major groove. An increase in the diameter of the DNA at the pseudoplatform formed by the cross-linked residues creates an A-DNA characteristic hole in the central portion of the DNA. This results in a centrally underwound base step and a number of subsequent overwinding steps leading to an overall axis bend toward the major groove. The structure shows narrowing of both minor and major grooves in the proximity of the cross-link. The perturbation leads to preferential intrastrand base stacking, disruption of adjacent canonical (A.T) base pairing, and buckling of base pairs, the extent of which diminishes with progression away from the lesion site. Overall, the distortion induced by the cross-link spreads over three base pairs on the 5'- and 3'-sides of the cross-link.


    Organizational Affiliation

    Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'B11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
D00
Query on D00
B
DNA LINKINGC11 H18 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: the structure submitted is the lowest energy structure of a an ensemble of selected ten structures 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-06-25
    Type: Structure summary