3L2C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.868 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


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.,Sect.D 66: 1351-1357

  • DOI: 10.1107/S0907444910042228

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Forkhead box protein O4
A
110Homo sapiensMutation(s): 0 
Gene Names: FOXO4 (AFX, AFX1, MLLT7)
Find proteins for P98177 (Homo sapiens)
Go to Gene View: FOXO4
Go to UniProtKB:  P98177
Entity ID: 1
MoleculeChainsLengthOrganism
FOXO consensus binding sequence, plus strandB13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
FOXO consensus binding sequence, minus strandC13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.868 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 40.810α = 90.00
b = 71.700β = 90.00
c = 131.860γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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