Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex

Nat Struct Biol. 1998 Aug;5(8):692-7. doi: 10.1038/1382.


Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein-DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain-DNA interactions.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antennapedia Homeodomain Protein
  • Asparagine / chemistry
  • Binding Sites
  • Crystallography, X-Ray
  • DNA / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Homeodomain Proteins / chemistry*
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Nuclear Proteins*
  • Nucleotides / chemistry
  • Sugar Phosphates / chemistry
  • Transcription Factors*


  • Antennapedia Homeodomain Protein
  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Nuclear Proteins
  • Nucleotides
  • Sugar Phosphates
  • Transcription Factors
  • Asparagine
  • DNA

Associated data

  • PDB/9ANT