1MDW | pdb_00001mdw

Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation

• PDB DOI: https://doi.org/10.2210/pdb1MDW/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-08-07 Released: 2003-04-29 
• Deposition Author(s): Moldoveanu, T., Hosfield, C.M., Lim, D., Jia, Z., Davies, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 

Literature

Calpain silencing by a reversible intrinsic mechanism.

Moldoveanu, T., Hosfield, C.M., Lim, D., Jia, Z., Davies, P.L.

(2003) Nat Struct Biol 10: 371-378

• PubMed: 12665854 
• DOI: https://doi.org/10.1038/nsb917
• Primary Citation Related Structures: 
  1MDW


• PubMed Abstract: 
  

  Uncontrolled activation of calpain can lead to necrotic cell death and irreversible tissue damage. We have discovered an intrinsic mechanism whereby the autolysis-generated protease core fragment of calpain is inactivated through the inherent instability of a key alpha-helix. This auto-inactivation state was captured by the 1.9 A Ca(2+)-bound structure of the protease core from m-calpain, and sequence alignments suggest that it applies to about half of the calpain isoforms. Intact calpain large subunits are also subject to this inhibition, which can be prevented through assembly of the heterodimers. Other isoforms or their released cores are not silenced by this mechanism and might contribute to calpain patho-physiologies.

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Organizational Affiliation: 
• Department of Biochemistry and the Protein Engineering Network of Centres of Excellence, Queen's University, Kingston, Ontario K7L 3N6, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.78 kDa 
• Atom Count: 5,409 
• Modeled Residue Count: 637 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain II, catalytic subunit	A, B	328	Rattus norvegicus	Mutation(s): 1  Gene Names: CALPAIN II EC: 3.4.22.17 (PDB Primary Data), 3.4.22.53 (UniProt)
UniProt
Find proteins for Q07009 (Rattus norvegicus) Explore Q07009  Go to UniProtKB:  Q07009

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.6	α = 90
b = 80.6	β = 103.9
c = 75.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-29 
Deposition Author(s): Moldoveanu, T., Hosfield, C.M., Lim, D., Jia, Z., Davies, P.L.

Revision History  

• Version 1.0: 2003-04-29
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection