3AJL

Crystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:guanosine Base-pair in B-DNA with DAPI

• PDB DOI: https://doi.org/10.2210/pdb3AJL/pdb
• NAKB: 3AJL

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2011-04-27 
• Deposition Author(s): Tsunoda, M., Sakaue, T., Ueno, Y., Matsuda, A., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil

Tsunoda, M., Sakaue, T., Naito, S., Sunami, T., Abe, N., Ueno, Y., Matsuda, A., Takenaka, A.

(2010) J Nucleic Acids 2010: 107289-107289

• PubMed: 20976303 
• DOI: https://doi.org/10.4061/2010/107289
• Primary Citation of Related Structures:  
  3AJJ, 3AJK, 3AJL


• PubMed Abstract: 
  

  Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

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Organizational Affiliation: 

Faculty of Pharmacy, Iwaki Meisei University, Chuodai-Iino, Iwaki 970-8551, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.69 kDa 
• Atom Count: 557 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAP	C [auth A]	6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE C16 H15 N5 FWBHETKCLVMNFS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.281 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.003	α = 90
b = 40.501	β = 90
c = 66.773	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
DPS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Tsunoda, M., Sakaue, T., Ueno, Y., Matsuda, A., Takenaka, A.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description