294D

INTERCALATED CYTOSINE MOTIF AND NOVEL ADENINE CLUSTERS IN THE CRYSTAL STRUCTURE OF TETRAHYMENA TELOMERE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere.

Cai, L.Chen, L.Raghavan, S.Ratliff, R.Moyzis, R.Rich, A.

(1998) Nucleic Acids Res 26: 4696-4705

  • DOI: 10.1093/nar/26.20.4696
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The cytosine-rich strand of the Tetrahymena telomere consists of multiple repeats of sequence d(AACCCC). We have solved the crystal structure of the crystalline repeat sequence at 2.5 A resolution. The adenines form two different and previously unkno ...

    The cytosine-rich strand of the Tetrahymena telomere consists of multiple repeats of sequence d(AACCCC). We have solved the crystal structure of the crystalline repeat sequence at 2.5 A resolution. The adenines form two different and previously unknown clusters (A clusters) in orthogonal directions with their counterparts from other strands, each containing a total of eight adenines. The clusters appear to be stable aggregates held together by base stacking and three different base-pairing modes. Two different types of cytosine tetraplexes are found in the crystal. Each four-stranded complex is composed of two intercalated parallel-stranded duplexes pointing in opposite directions, with hemiprotonated cytosine-cytosine (C.C+) base pairs. The outermost C.C+base pairs are from the 5'-end of each strand in one cytosine tetraplex and from the 3'-end of each strand in the other. The A clusters and the cytosine tetraplexes form two alternating stacking patterns, creating continuous base stacking in two perpendicular directions along the x - and z -axes. The adenine clusters could be organizational motifs for macromolecular RNA.


    Related Citations: 
    • Crystal Structure of a Four-Stranded Intercalated DNA: d(C4)
      Chen, L., Cai, L., Zhang, X., Rich, A.
      (1994) Biochemistry 33: 13540

    Organizational Affiliation

    Department of Biology, Room 68-233, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*CP*CP*C)-3')A, B,C,D,E,F,G,H6N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.93α = 90
b = 52.33β = 90
c = 76.94γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
PROCESSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-19
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance