376D

A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.

Shepard, W.Cruse, W.B.Fourme, R.de la Fortelle, E.Prange, T.

(1998) Structure 6: 849-861


  • PubMed Abstract: 
  • The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive seque ...

    The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood.


    Related Citations: 
    • Extraordinary Stable Structure of Short Single-Stranded DNA Fragments Containing a Specific Base Sequence: d(GCGAAAGC)
      Hirao, I.,Nichimura, Y.,Naraoka, T.,Watanabe, K.,Arata, Y.,Miura, K.
      (1989) Nucleic Acids Res. 17: 2223
    • Solution Structure of a Metal-binding Site in the Major Groove of RNA Complexed with Cobalt(III) Hexammine
      Kieft, J.S.,Tinoco Jr., I.
      (1997) Structure 5: 713
    • Structural Basis for Stabilisation of Z-DNA by Cobalt Haxaammine and Magnesium Cations
      Geissner, R.V.,Quigley, G.J.,Wang, H.J.,van der Marel, A.,van Boom, J.H.
      (1985) Biochemistry 24: 237
    • RNA Tertiary Structure Mediation by Adenosine Platforms
      Cate, J.H.,Gooding, A.R.,Podell, E.,Zhou, K.,Golden, B.L.,Szewczak, A.A.,Kundrot, C.E.,Cech, T.R.,Doudna, J.A.
      (1997) Science 273: 1696


    Organizational Affiliation

    LURE, Université Paris-Sud, Orsay, France. shepard@lure.u-psud.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*(CBR)P*GP*AP*AP*AP*GP*CP*T)-3')A9N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 37.560α = 90.00
b = 37.560β = 90.00
c = 65.390γ = 120.00
Software Package:
Software NamePurpose
CCP4phasing
X-PLORrefinement
MOSFLMdata reduction
MADLSQmodel building
CCP4data scaling
MADLSQphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-26
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance