1BQJ

CRYSTAL STRUCTURE OF D(ACCCT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 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.,Sect.D 55: 422-429

  • Primary Citation of Related Structures:  

  • 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 ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*CP*T)-3')A,B,C,D5N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 93.810α = 90.00
b = 93.810β = 90.00
c = 93.810γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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