Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha

J Mol Biol. 2000 Apr 14;297(5):1183-94. doi: 10.1006/jmbi.2000.3642.


Importin-alpha is the nuclear import receptor that recognizes cargo proteins which contain classical monopartite and bipartite nuclear localization sequences (NLSs), and facilitates their transport into the nucleus. To determine the structural basis of the recognition of the two classes of NLSs by mammalian importin-alpha, we co-crystallized an N-terminally truncated mouse receptor protein with peptides corresponding to the monopartite NLS from the simian virus 40 (SV40) large T-antigen, and the bipartite NLS from nucleoplasmin. We show that the monopartite SV40 large T-antigen NLS binds to two binding sites on the receptor, similar to what was observed in yeast importin-alpha. The nucleoplasmin NLS-importin-alpha complex shows, for the first time, the mode of binding of bipartite NLSs to the receptor. The two basic clusters in the NLS occupy the two binding sites used by the monopartite NLS, while the sequence linking the two basic clusters is poorly ordered, consistent with its tolerance to mutations. The structures explain the structural basis for binding of diverse NLSs to the sole receptor protein.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Conserved Sequence
  • Crystallography, X-Ray
  • Karyopherins
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation / genetics
  • Nuclear Localization Signals / physiology*
  • Nuclear Proteins / antagonists & inhibitors
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • Nucleoplasmins
  • Oligopeptides / chemistry
  • Oligopeptides / metabolism*
  • Peptide Fragments / antagonists & inhibitors
  • Peptide Fragments / chemistry
  • Peptide Fragments / genetics
  • Peptide Fragments / metabolism
  • Phosphoproteins / chemistry*
  • Phosphoproteins / metabolism*
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Structure-Activity Relationship
  • Substrate Specificity
  • Yeasts / chemistry


  • Karyopherins
  • Nuclear Localization Signals
  • Nuclear Proteins
  • Nucleoplasmins
  • Oligopeptides
  • Peptide Fragments
  • Phosphoproteins
  • SV40 nuclear localization peptide

Associated data

  • PDB/1EJY