Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins

Genes Dev. 2010 Oct 15;24(20):2270-5. doi: 10.1101/gad.1976610. Epub 2010 Sep 28.


Early B-cell factor 1 (Ebf1) is a key transcriptional determinant of B-lymphocyte differentiation whose DNA-binding domain has no sequence similarity to other transcription factor families. Here we report the crystal structure of an Ebf1 dimer bound to its palindromic recognition site. The DNA-binding domain adopts a pseudoimmunoglobulin-like fold with novel topology, but is structurally similar to the Rel homology domains of NFAT and NF-κB. Ebf1 contacts the DNA with two loop-based modules and a unique Zn coordination motif whereby each Ebf1 monomer interacts with both palindromic half-sites. This unusual mode of DNA recognition generates an extended contact area that may be crucial for the function of Ebf1 in chromatin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites / drug effects
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism*
  • Electrophoresis, Polyacrylamide Gel
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proto-Oncogene Proteins c-rel / chemistry
  • Proto-Oncogene Proteins c-rel / genetics
  • Proto-Oncogene Proteins c-rel / metabolism*
  • Trans-Activators / chemistry
  • Trans-Activators / genetics
  • Trans-Activators / metabolism*
  • Zinc / chemistry
  • Zinc / metabolism


  • Ebf1 protein, mouse
  • Proto-Oncogene Proteins c-rel
  • Trans-Activators
  • DNA
  • Zinc