1QP5

BASE-PAIRING SHIFT IN A DODECAMER CONTAINING A (CA)N TRACT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures.

Timsit, Y.Vilbois, E.Moras, D.

(1991) Nature 354: 167-170

  • DOI: 10.1038/354167a0
  • Primary Citation of Related Structures:  
  • Also Cited By: 1VTD

  • PubMed Abstract: 
  • the crystal packing of the B-DNA dodecamer d(ACCG-GCGCCACA).d(TGTGGCGCCGGT) is characterized by the reciprocal fit of double helices with specific base-backbone interactions in the major groove. Cooling the crystals below -10 degrees C stabilizes a n ...

    the crystal packing of the B-DNA dodecamer d(ACCG-GCGCCACA).d(TGTGGCGCCGGT) is characterized by the reciprocal fit of double helices with specific base-backbone interactions in the major groove. Cooling the crystals below -10 degrees C stabilizes a new conformational state with a long-range sequence-dependent one-step shift in the major-groove base pairing. The tilt of the bases leads to the disruption of the Watson-Crick pairing in the major groove and to the formation of interactions with the 5' neighbour of their complement. This alteration propagates along the helical axis over more than half a turn. As a result, the molecular structure is normal when seen from the minor groove side and mismatched in the major groove. Comparison with a parent isomorphous dodecamer structure corresponding to the codon 10-13 of the c-Ha-ras proto-oncogene show that this new structural feature is sequence dependent and clearly favoured by (CA)n tracts. As(CA)n tracts of DNA are involved both in recombination and in transcription, this new recognition pattern should be considered in the analysis of the various processes involving the reading of the genetic information.


    Related Citations: 
    • Self-fitting and self-modifying properties of the B-DNA molecule
      Timsit, Y.,Moras, D.
      (1995) J.Mol.Biol. 251: 629


    Organizational Affiliation

    Laboratoire de Cristallographie Biologique, Institut de Biologie Mol├ęculaire et Cellulaire, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3')A12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 65.900α = 90.00
b = 65.900β = 90.00
c = 47.100γ = 120.00
Software Package:
Software NamePurpose
ULTIMAphasing
NUCLSQrefinement
X-GENdata scaling
ULTIMAmodel building
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description