1KFX

Crystal Structure of Human m-Calpain Form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium.

Strobl, S.Fernandez-Catalan, C.Braun, M.Huber, R.Masumoto, H.Nakagawa, K.Irie, A.Sorimachi, H.Bourenkow, G.Bartunik, H.Suzuki, K.Bode, W.

(2000) Proc Natl Acad Sci U S A 97: 588-592

  • DOI: 10.1073/pnas.97.2.588
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Calpains (calcium-dependent cytoplasmic cysteine proteinases) are implicated in processes such as cytoskeleton remodeling and signal transduction. The 2.3-A crystal structure of full-length heterodimeric [80-kDa (dI-dIV) + 30-kDa (dV+dVI)] human m-ca ...

    Calpains (calcium-dependent cytoplasmic cysteine proteinases) are implicated in processes such as cytoskeleton remodeling and signal transduction. The 2.3-A crystal structure of full-length heterodimeric [80-kDa (dI-dIV) + 30-kDa (dV+dVI)] human m-calpain crystallized in the absence of calcium reveals an oval disc-like shape, with the papain-like catalytic domain dII and the two calmodulin-like domains dIV+dVI occupying opposite poles, and the tumor necrosis factor alpha-like beta-sandwich domain dIII and the N-terminal segments dI+dV located between. Compared with papain, the two subdomains dIIa+dIIb of the catalytic unit are rotated against one another by 50 degrees, disrupting the active site and the substrate binding site, explaining the inactivity of calpains in the absence of calcium. Calcium binding to an extremely negatively charged loop of domain dIII (an electrostatic switch) could release the adjacent barrel-like subdomain dIIb to move toward the helical subdomain dIIa, allowing formation of a functional catalytic center. This switch loop could also mediate membrane binding, thereby explaining calpains' strongly reduced calcium requirements in vivo. The activity status at the catalytic center might be further modulated by calcium binding to the calmodulin domains via the N-terminal linkers.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of recombinant full-length m-calpain
      Masumoto, H., Nakagawa, K., Irie, S., Sorimachi, H., Suzuki, K., Bourenkow, G., Bartunik, H., Fernandez-Catalan, C., Bode, W., Strobl, S.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 73
    • Structural basis for possible calcium-induced activation mechanisms of calpains
      Reverter, D., Strobl, S., Fernandez-Catalan, C., Sorimachi, H., Suzuki, K., Bode, W.
      (2001) Biol Chem 382: 753
    • The structure of calcium-free human m-calpain
      Reverter, D., Sorimachi, H., Bode, W.
      (2001) Trends Cardiovasc Med 11: 222

    Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Am Klopferspitz 18a, D 82 152 Planegg-Martinsried, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M-CALPAIN LARGE SUBUNITL699Homo sapiensMutation(s): 0 
Gene Names: CAPN2CANPL2
EC: 3.4.22.53
Find proteins for P17655 (Homo sapiens)
Explore P17655 
Go to UniProtKB:  P17655
NIH Common Fund Data Resources
PHAROS  P17655
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
M-CALPAIN SMALL SUBUNITS184Homo sapiensMutation(s): 0 
Gene Names: CAPNS1CAPN4CAPNS
Find proteins for P04632 (Homo sapiens)
Explore P04632 
Go to UniProtKB:  P04632
NIH Common Fund Data Resources
PHAROS  P04632
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.78α = 90
b = 133.25β = 102.07
c = 77.53γ = 90
Software Package:
Software NamePurpose
MAINmodel building
CNSrefinement
DENZOdata reduction
CCP4data scaling
MAINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-02
    Changes: Structure summary