3CRX

CRE RECOMBINASE/DNA COMPLEX INTERMEDIATE I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination.

Gopaul, D.N.Guo, F.Van Duyne, G.D.

(1998) EMBO J. 17: 4175-4187

  • DOI: 10.1093/emboj/17.14.4175
  • Primary Citation of Related Structures:  2CRX

  • PubMed Abstract: 
  • We have determined the X-ray crystal structures of two DNA Holliday junctions (HJs) bound by Cre recombinase. The HJ is a four-way branched structure that occurs as an intermediate in genetic recombination pathways, including site-specific recombinat ...

    We have determined the X-ray crystal structures of two DNA Holliday junctions (HJs) bound by Cre recombinase. The HJ is a four-way branched structure that occurs as an intermediate in genetic recombination pathways, including site-specific recombination by the lambda-integrase family. Cre recombinase is an integrase family member that recombines 34 bp loxP sites in the absence of accessory proteins or auxiliary DNA sequences. The 2.7 A structure of Cre recombinase bound to an immobile HJ and the 2.5 A structure of Cre recombinase bound to a symmetric, nicked HJ reveal a nearly planar, twofold-symmetric DNA intermediate that shares features with both the stacked-X and the square conformations of the HJ that exist in the unbound state. The structures support a protein-mediated crossover isomerization of the junction that acts as the switch responsible for activation and deactivation of recombinase active sites. In this model, a subtle isomerization of the Cre recombinase-HJ quaternary structure dictates which strands are cleaved during resolution of the junction via a mechanism that involves neither branch migration nor helical restacking.


    Related Citations: 
    • Structure of Cre Recombinase Complexed with DNA in a Site-Specific Recombination Synapse
      Guo, F.,Gopaul, D.N.,Van Duyne, G.D.
      (1997) Nature 389: 40


    Organizational Affiliation

    Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CRE RECOMBINASE
A, B
343Enterobacteria phage P1Gene Names: cre
Find proteins for P06956 (Enterobacteria phage P1)
Go to UniProtKB:  P06956
Entity ID: 1
MoleculeChainsLengthOrganism
DNA 35-MERC35N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 35-MERD35N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 35-MERE35N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA 35-MERF35N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 106.300α = 90.00
b = 122.700β = 90.00
c = 179.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance