1BQJ

CRYSTAL STRUCTURE OF D(ACCCT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT).

Weil, J.Min, T.Yang, C.Wang, S.Sutherland, C.Sinha, N.Kang, C.

(1999) Acta Crystallogr D Biol Crystallogr 55: 422-429

  • DOI: 10.1107/s0907444998012529
  • Primary Citation of Related Structures:  
    1BQJ, 1CN0

  • PubMed Abstract: 
  • The crystal structure of d(ACCCT), solved by molecular replacement, shows a four-stranded i-motif conformation, where two parallel duplexes intercalate with one another in opposite orientations. Each duplex is stabilized by hemi-protonated C-C+ base pairing between parallel strands, and a string of water molecules bridge the cytosine N4 atoms to phosphate O atoms ...

    The crystal structure of d(ACCCT), solved by molecular replacement, shows a four-stranded i-motif conformation, where two parallel duplexes intercalate with one another in opposite orientations. Each duplex is stabilized by hemi-protonated C-C+ base pairing between parallel strands, and a string of water molecules bridge the cytosine N4 atoms to phosphate O atoms. This structure of d(ACCCT) shows examples of reversed Hoogsteen and Watson-Crick base pairing in both intermolecular and intramolecular manners to stabilize the tetraplex. Noticeably, the four-stranded complex is further stabilized at one end by a three-base hydrogen-bonding network, in which two adenines and a thymine form four hydrogen bonds via a reverse Hoogsteen and an asymmetric adenine-adenine base pairing. The structure of d(ACCCT) shows a similar local structure to that found in the d(TAA) part of the crystal structure of d(TAACCC) and provides further structural evidence that these base arrangements are essential for stabilizing these novel DNA super-secondary structures.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Washington State University, Pullman, WA 99164-4660, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*CP*CP*T)-3')A, B, C, D5N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.235 
    • R-Value Work: 0.192 
    • R-Value Observed: 0.192 
    • Space Group: I 2 3
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 93.81α = 90
    b = 93.81β = 90
    c = 93.81γ = 90
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-03-18
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance