Structure of a novel winged-helix like domain from human NFRKB protein

PLoS One. 2012;7(9):e43761. doi: 10.1371/journal.pone.0043761. Epub 2012 Sep 11.


The human nuclear factor related to kappa-B-binding protein (NFRKB) is a 1299-residue protein that is a component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. Although full length NFRKB is predicted to be around 65% disordered, comparative sequence analysis identified several potentially structured sections in the N-terminal region of the protein. These regions were targeted for crystallographic studies, and the structure of one of these regions spanning residues 370-495 was determined using the JCSG high-throughput structure determination pipeline. The structure reveals a novel, mostly helical domain reminiscent of the winged-helix fold typically involved in DNA binding. However, further analysis shows that this domain does not bind DNA, suggesting it may belong to a small group of winged-helix domains involved in protein-protein interactions.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Crystallography, X-Ray
  • Cullin Proteins / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • Humans
  • Molecular Sequence Data
  • Protein Binding
  • Protein Denaturation
  • Protein Interaction Maps
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry
  • Saccharomyces cerevisiae / chemistry
  • Sequence Alignment
  • Structural Homology, Protein
  • Temperature
  • Winged-Helix Transcription Factors / chemistry*


  • Bacterial Proteins
  • Cullin 1
  • Cullin Proteins
  • DNA-Binding Proteins
  • MecI protein, Staphylococcus
  • NFRKB protein, human
  • Repressor Proteins
  • Winged-Helix Transcription Factors
  • DNA

Associated data

  • PDB/3U21