Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities

Structure. 2017 Oct 3;25(10):1598-1610.e3. doi: 10.1016/j.str.2017.07.017. Epub 2017 Sep 7.


SH3 domains are protein modules that mediate protein-protein interactions in many eukaryotic signal transduction pathways. The majority of SH3 domains studied thus far act by binding to proline-rich sequences in partner proteins, but a growing number of studies have revealed alternative recognition mechanisms. We have comprehensively surveyed the specificity landscape of human SH3 domains in an unbiased manner using peptide-phage display and deep sequencing. Based on ∼70,000 unique binding peptides, we obtained 154 specificity profiles for 115 SH3 domains, which reveal that roughly half of the SH3 domains exhibit non-canonical specificities and collectively recognize a wide variety of peptide motifs, most of which were previously unknown. Crystal structures of SH3 domains with two distinct non-canonical specificities revealed novel peptide-binding modes through an extended surface outside of the canonical proline-binding site. Our results constitute a significant contribution toward a complete understanding of the mechanisms underlying SH3-mediated cellular responses.

Keywords: ITSN1; SH3 domain; SORBS2; atypical binding; deep sequencing; domain specificity; peptide library; peptide motif; peptide-recognition module; phage display.

Publication types

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

MeSH terms

  • Animals
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Models, Molecular
  • Peptide Library
  • Peptides / metabolism
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism*
  • Sequence Analysis, Protein / methods*
  • src Homology Domains


  • Peptide Library
  • Peptides
  • Proteins