A novel DNA recognition mode by the NF-kappa B p65 homodimer

Nat Struct Biol. 1998 Jan;5(1):67-73. doi: 10.1038/nsb0198-67.


The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • DNA-Binding Proteins / chemistry*
  • Deoxyribonucleoproteins / chemistry*
  • Dimerization
  • Humans
  • Hydrogen Bonding
  • Mice
  • Molecular Sequence Data
  • NF-kappa B / chemistry*
  • NF-kappa B / ultrastructure
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Proteins
  • Structure-Activity Relationship


  • DNA-Binding Proteins
  • Deoxyribonucleoproteins
  • NF-kappa B
  • Recombinant Proteins

Associated data

  • PDB/1RAM
  • PDB/2RAM