Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101231.88 
• Atom Count: 7119 
• Residue Count: 883 
• Unique protein chains: 2

1KFU

Crystal Structure of Human m-Calpain Form II

• DOI: 10.2210/pdb1KFU/pdb
• Entry 1KFU supersedes 1DKV

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2001-11-23 Released: 2001-12-07 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.276 
• R-Value Work: 0.221 

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

• PubMed: 10639123 
• Primary Citation of Related Structures:  
  1KFX
• 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-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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
M-CALPAIN LARGE SUBUNIT	L	699	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
M-CALPAIN SMALL SUBUNIT	S	184	Homo sapiens	Mutation(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 = 51.880	α = 90.00
b = 169.840	β = 95.12
c = 64.440	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
CNS	refinement
CNS	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-23 
• Released Date: 2001-12-07 
• Deposition Author(s): 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.
• This entry supersedes: 1DKV

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