1KFU

Crystal Structure of Human m-Calpain Form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 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.USA 97: 588-592

  • Primary Citation of Related Structures:  
  • Also Cited By: 3DF0

  • 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: 
    • The structure of calcium-free human m-calpain
      Reverter, D.,Sorimachi, H.,Bode, W.
      (2001) Trends Cardiovasc.Med. 11: 222
    • 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.,Sect.D 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


    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 SUBUNIT
L
699Homo sapiensMutation(s): 0 
Gene Names: CAPN2 (CANPL2)
EC: 3.4.22.53
Find proteins for P17655 (Homo sapiens)
Go to Gene View: CAPN2
Go to UniProtKB:  P17655
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
M-CALPAIN SMALL SUBUNIT
S
184Homo sapiensMutation(s): 0 
Gene Names: CAPNS1 (CAPN4, CAPNS)
Find proteins for P04632 (Homo sapiens)
Go to Gene View: CAPNS1
Go to UniProtKB:  P04632
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.880α = 90.00
b = 169.840β = 95.12
c = 64.440γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSrefinement
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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