1FHZ | pdb_00001fhz

PSORALEN CROSS-LINKED D(CCGGTACCGG) FORMS HOLLIDAY JUNCTION

• PDB DOI: https://doi.org/10.2210/pdb1FHZ/pdb
• NAKB: 1FHZ

• Classification: DNA
• Mutation(s): No 


• Deposited: 2000-08-02 Released: 2001-04-21 
• Deposition Author(s): Eichman, B.F., Mooers, B.H.M., Alberti, M., Hearst, J.E., Ho, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.311 (Depositor) 
• R-Value Work: 
  0.228 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

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 Biology 308: 15-26

• PubMed: 11302703 
• DOI: https://doi.org/10.1006/jmbi.2001.4567
• Primary Citation Related Structures: 
  1FHY, 1FHZ


• 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-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.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.35 kDa 
• Atom Count: 466 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PSO	C [auth B]	4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN C15 H14 O4 RGJSDHXSAKMPNM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.311 (Depositor) 
• R-Value Work:  0.228 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.116	α = 90
b = 23.651	β = 112.64
c = 36.182	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-21 
Deposition Author(s): Eichman, B.F., Mooers, B.H.M., Alberti, M., Hearst, J.E., Ho, P.S.

Revision History  

• Version 1.0: 2001-04-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations