2IIE

single chain Integration Host Factor protein (scIHF2) in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending

Bao, Q.Chen, H.Liu, Y.Yan, J.Droge, P.Davey, C.A.

(2007) J Mol Biol 367: 731-740

  • DOI: 10.1016/j.jmb.2006.09.082
  • Primary Citation of Related Structures:  
    2IIF, 2IIE

  • PubMed Abstract: 
  • Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found to adopt two stable conformational states in complex with a specific DNA target ...

    Architectural proteins that reconfigure the paths of DNA segments are required for the establishment of functional interfaces in many genomic transactions. A single-chain derivative of the DNA architectural protein integration host factor was found to adopt two stable conformational states in complex with a specific DNA target. In the so-called open state, the degree of protein-induced DNA bending is reduced significantly compared with the closed state. The conformational switch between these states is controlled by divalent metal binding in two electronegative zones arising from the lysine-to-glutamate substitution in the protein body proximal to the phosphate backbone of one DNA arm. We show that this switch can be employed to control the efficiency of site-specific recombination catalyzed by lambda integrase. Introduction of acidic residues at the protein-DNA interface holds potential for the design of metal-mediated switches for the investigation of functional relationships.


    Related Citations: 
    • Activation of site-specific DNA integration in human cells by a single chain integration host factor
      Corona, T., Bao, Q., Christ, N., Schwartz, T., Li, J., Droege, P.
      (2003) Nucleic Acids Res 31: 5140
    • Single-chain integration host factors as probes for high-precision nucleoprotein complex formation
      Bao, Q., Christ, N., Droege, P.
      (2004) Gene 343: 99

    Organizational Affiliation

    Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Integration host factor A204Escherichia coliMutation(s): 0 
Find proteins for P0A6X7 (Escherichia coli (strain K12))
Explore P0A6X7 
Go to UniProtKB:  P0A6X7
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
Explore P0A6Y1 
Go to UniProtKB:  P0A6Y1
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Phage P H' siteC35synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DGP*DGP*DCP*DCP*DAP*DAP*DAP*DAP*DAP*DAP*DGP*DCP*DAP*DTP*DT)-3')D15synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DGP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DC)-3')E20synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.41 Å
      • R-Value Free: 0.272 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.234 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 47.371α = 90
      b = 55.311β = 90
      c = 177.833γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      PDB_EXTRACTdata extraction
      CrystalCleardata collection
      CCP4phasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2007-02-20
        Type: Initial release
      • Version 1.1: 2008-05-01
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2017-08-09
        Changes: Source and taxonomy
      • Version 1.4: 2017-08-16
        Changes: Source and taxonomy