2DZ7 | pdb_00002dz7

DNA Octaplex Formation with an I-Motif of A-Quartets: The Revised Crystal Structure of d(GCGAAAGC)

• PDB DOI: https://doi.org/10.2210/pdb2DZ7/pdb
• NAKB: 2DZ7

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-09-21 Released: 2007-08-14 
• Deposition Author(s): Sato, Y., Mitomi, K., Sumani, T., Kondo, J., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.211 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC)

Sato, Y., Mitomi, K., Sunami, T., Kondo, J., Takenaka, A.

(2006) J Biochem 140: 759-762

• PubMed: 17062599 
• DOI: https://doi.org/10.1093/jb/mvj213
• Primary Citation Related Structures: 
  2DZ7


• PubMed Abstract: 
  

  The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

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Organizational Affiliation: 
• Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuda, Midori-ku, Yokohama 226-850.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.51 kDa 
• Atom Count: 259 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3')	A	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.211 (Depositor) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.909	α = 90
b = 36.909	β = 90
c = 64.337	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Sato, Y., Mitomi, K., Sumani, T., Kondo, J., Takenaka, A.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description