Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin

EMBO J. 1993 Jul;12(7):2617-24. doi: 10.2210/pdb1shf/pdb.


The Src-homology 3 (SH3) region is a protein domain consisting of approximately 60 residues. It occurs in a large number of eukaryotic proteins involved in signal transduction, cell polarization and membrane--cytoskeleton interactions. The function is unknown, but it is probably involved in specific protein--protein interactions. Here we report the crystal structure of the SH3 domain of Fyn (a Src family tyrosine kinase) at 1.9 A resolution. The crystals have two SH3 molecules per asymmetric unit. These two Fyn SH3 domains are not related by a local twofold axis. The crystal structures of spectrin and Fyn SH3 domains as well as the solution structure of the Src SH3 domain show that these all have the same basic fold. A protein domain which has the same topology as SH3 is present in the prokaryotic regulatory enzyme BirA. The comparison between the crystal structures of Fyn and spectrin SH3 domains shows that a conserved surface patch, consisting mainly of aromatic residues, is flanked by two hairpin-like loops (residues 94-104 and 114-118 in Fyn). These loops are different in tyrosine kinase and spectrin SH3 domains. They could modulate the binding properties of the aromatic surface.

MeSH terms

  • Bacterial Proteins / chemistry
  • Base Sequence
  • Binding Sites
  • Carbon-Nitrogen Ligases*
  • Escherichia coli Proteins*
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Oligodeoxyribonucleotides
  • Protein Conformation
  • Protein-Tyrosine Kinases / chemistry*
  • Proto-Oncogene Proteins / chemistry*
  • Proto-Oncogene Proteins c-fyn
  • Proto-Oncogene Proteins pp60(c-src) / chemistry*
  • Repressor Proteins / chemistry
  • Spectrin / chemistry*
  • Transcription Factors*
  • X-Ray Diffraction


  • Bacterial Proteins
  • Escherichia coli Proteins
  • Ligands
  • Oligodeoxyribonucleotides
  • Proto-Oncogene Proteins
  • Repressor Proteins
  • Transcription Factors
  • Spectrin
  • Protein-Tyrosine Kinases
  • FYN protein, human
  • Proto-Oncogene Proteins c-fyn
  • Proto-Oncogene Proteins pp60(c-src)
  • Carbon-Nitrogen Ligases
  • birA protein, E coli