4PZQ

Crystal Structure of CCG DNA repeats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats

Chen, Y.W.Jhan, C.R.Neidle, S.Hou, M.H.

(2014) Angew Chem Int Ed Engl 53: 10682-10686

  • DOI: https://doi.org/10.1002/anie.201405637
  • Primary Citation of Related Structures:  
    4PZQ

  • PubMed Abstract: 

    CCG triplet repeats can fold into tetraplex structures, which are associated with the expansion of (CCG)n trinucleotide sequences in certain neurological diseases. These structures are stabilized by intertwining i-motifs. However, the structural basis for tetraplex i-motif formation in CCG triplet repeats remains largely unknown. We report the first crystal structure of a CCG-repeat sequence, which shows that two dT(CCG)3 A strands can associate to form a tetraplex structure with an i-motif core containing four C:C(+) pairs flanked by two G:G homopurine base pairs as a structural motif. The tetraplex core is attached to a short parallel-stranded duplex. Each hairpin itself contains a central CCG loop in which the nucleotides are flipped out and stabilized by stacking interactions. The helical twists between adjacent cytosine residues of this structure in the i-motif core have an average value of 30°, which is greater than those previously reported for i-motif structures.


  • Organizational Affiliation

    Institute of Genomics and Bioinformatics and Institute of Biochemistry, National Chung Hsing University, No. 250 Kuo-Kuang Road, Taichung (Taiwan).


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')11Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.145α = 90
b = 38.145β = 90
c = 54.249γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations