1FHZ

PSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions.

Eichman, B.F.Mooers, B.H.Alberti, M.Hearst, J.E.Ho, P.S.

(2001) J.Mol.Biol. 308: 15-26

  • DOI: 10.1006/jmbi.2001.4567
  • Primary Citation of Related Structures:  1FHY

  • PubMed Abstract: 
  • The single-crystal structures are presented for two DNA sequences with the thymine bases covalently cross-linked across the complementary strands by 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT). The HMT-adduct of d(CCGCTAGCGG) forms a psoralen-ind ...

    The single-crystal structures are presented for two DNA sequences with the thymine bases covalently cross-linked across the complementary strands by 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT). The HMT-adduct of d(CCGCTAGCGG) forms a psoralen-induced Holliday junction, showing for the first time the effect of this important class of chemotheraputics on the structure of the recombination intermediate. In contrast, HMT-d(CCGGTACCGG) forms a sequence-dependent junction. In both structures, the DNA duplex is highly distorted at the thymine base linked to the six-member pyrone ring of the drug. The psoralen cross-link defines the intramolecular interactions of the drug-induced junction, while the sequence-dependent structure is nearly identical to the native Holliday junction of d(CCGGTACCGG) alone. The two structures contrast the effects of drug- and sequence-dependent interactions on the structure of a Holliday junction, suggesting a role for psoralen in the mechanism to initiate repair of psoralen-lesions in mammalian DNA.


    Related Citations: 
    • The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
      Eichman, B.F.,Vargason, J.M.,Mooers, B.H.M.,Ho, P.S.
      (2000) Proc.Natl.Acad.Sci.USA 97: 3971


    Organizational Affiliation

    Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')A,B10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PSO
Query on PSO

Download SDF File 
Download CCD File 
B
4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
C15 H14 O4
RGJSDHXSAKMPNM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.116α = 90.00
b = 23.651β = 112.64
c = 36.182γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance