3L2C

Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA

Boura, E., Rezabkova, L., Brynda, J., Obsilova, V., Obsil, T.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1351-1357

  • DOI: 10.1107/S0907444910042228
  • Primary Citation of Related Structures:  
    3L2C

  • PubMed Abstract: 

    • FOXO4 is a member of the FOXO subgroup of forkhead transcription factors that constitute key components of a conserved signalling pathway that connects growth and stress signals to transcriptional control. Here, the 1.9 Å resolution crystal structure of the DNA-binding domain of human FOXO4 (FOXO4-DBD) bound to a 13 bp DNA duplex containing a FOXO consensus binding sequence is reported ...

    FOXO4 is a member of the FOXO subgroup of forkhead transcription factors that constitute key components of a conserved signalling pathway that connects growth and stress signals to transcriptional control. Here, the 1.9 Å resolution crystal structure of the DNA-binding domain of human FOXO4 (FOXO4-DBD) bound to a 13 bp DNA duplex containing a FOXO consensus binding sequence is reported. The structure shows a similar recognition of the core sequence as has been shown for two other FOXO proteins. Helix H3 is docked into the major groove and provides all of the base-specific contacts, while the N-terminus and wing W1 make additional contacts with the phosphate groups of DNA. In contrast to other FOXO-DBD-DNA structures, the loop between helices H2 and H3 has a different conformation and participates in DNA binding. In addition, the structure of the FOXO4-DBD-DNA complex suggests that both direct water-DNA base contacts and the unique water-network interactions contribute to FOXO-DBD binding to the DNA in a sequence-specific manner.

    Organizational Affiliation: 

    Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Forkhead box protein O4C [auth A]110Homo sapiensMutation(s): 0 
Gene Names: AFX, AFX1, FOXO4, MLLT7
UniProt & NIH Common Fund Data Resources
Find proteins for P98177 (Homo sapiens)
Explore P98177 
Go to UniProtKB:  P98177
PHAROS:  P98177
GTEx:  ENSG00000184481
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    FOXO consensus binding sequence, plus strandA [auth B]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      FOXO consensus binding sequence, minus strandB [auth C]13N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      		 D [auth C], E [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.87 Å
      • R-Value Free: 0.228 
      • R-Value Work: 0.193 
      • R-Value Observed: 0.195 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 40.81α = 90
      b = 71.7β = 90
      c = 131.86γ = 90
      Software Package:
      Software NamePurpose
      SCALAdata scaling
      MOLREPphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      MAR345dtbdata collection
      MOSFLMdata reduction

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-12-29
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance