1KFU

Crystal Structure of Human m-Calpain Form II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 

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
  • Primary Citation of Related Structures:  
    1KFU, 1KFX

  • 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-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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M-CALPAIN LARGE SUBUNITA [auth L]699Homo sapiensMutation(s): 0 
Gene Names: CAPN2, CANPL2
EC: 3.4.22.53
UniProt & NIH Common Fund Data Resources
Find proteins for P17655 (Homo sapiens)
Explore P17655 
Go to UniProtKB:  P17655
PHAROS:  P17655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17655
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
M-CALPAIN SMALL SUBUNITB [auth S]184Homo sapiensMutation(s): 0 
Gene Names: CAPNS1, CAPN4, CAPNS
UniProt & NIH Common Fund Data Resources
Find proteins for P04632 (Homo sapiens)
Explore P04632 
Go to UniProtKB:  P04632
PHAROS:  P04632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04632
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.88α = 90
b = 169.84β = 95.12
c = 64.44γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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