Crystal structure of calpain-3 penta-EF-hand (PEF) domain - a homodimerized PEF family member with calcium bound at the fifth EF-hand

FEBS J. 2014 Jul;281(14):3138-49. doi: 10.1111/febs.12849. Epub 2014 Jun 9.


Calpains are Ca(2+) dependent intracellular cysteine proteases that cleave a wide range of protein substrates to help implement Ca(2+) signaling in the cell. The major isoforms of this enzyme family, calpain-1 and calpain-2, are heterodimers of a large and a small subunit, with the main dimer interface being formed through their C-terminal penta-EF hand (PEF) domains. Calpain-3, or p94, is a skeletal muscle-specific isoform that is genetically linked to limb-girdle muscular dystrophy. Biophysical and modeling studies with the PEF domain of calpain-3 support the suggestion that full-length calpain-3 exists as a homodimer. Here, we report the crystallization of calpain-3's PEF domain and its crystal structure in the presence of Ca(2+) , which provides evidence for the homodimer architecture of calpain-3 and supports the molecular model that places a protease core at either end of the elongated dimer. Unlike other calpain PEF domain structures, the calpain-3 PEF domain contains a Ca(2+) bound at the EF5-hand used for homodimer association. Three of the four Ca(2+) -binding EF-hands of the PEF domains are concentrated near the protease core, and have the potential to radically change the local charge within the dimer during Ca(2+) signaling. Examination of the homodimer interface shows that there would be steric clashes if the calpain-3 large subunit were to try to pair with a calpain small subunit. Database Structural data are available in the Protein Data Bank database under accession number 4OKH.

Keywords: calcium coordination; calpain; muscle-specific protease; muscular dystrophy; penta-EF-hand domain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Calcium / metabolism
  • Calcium Signaling
  • Calcium-Binding Proteins / metabolism
  • Calpain / chemistry*
  • Crystallization
  • Crystallography, X-Ray
  • EF Hand Motifs*
  • Models, Molecular
  • Molecular Sequence Data
  • Muscle Proteins / chemistry*
  • Protein Conformation
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Sequence Alignment


  • Calcium-Binding Proteins
  • Muscle Proteins
  • CAPN3 protein, human
  • Calpain
  • Calcium

Associated data

  • PDB/4OKH