3DF0

Calcium-dependent complex between m-calpain and calpastatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.

Moldoveanu, T.Gehring, K.Green, D.R.

(2008) Nature 456: 404-408

  • DOI: 10.1038/nature07353

  • PubMed Abstract: 
  • The Ca(2+)-dependent cysteine proteases, calpains, regulate cell migration, cell death, insulin secretion, synaptic function and muscle homeostasis. Their endogenous inhibitor, calpastatin, consists of four inhibitory repeats, each of which neutraliz ...

    The Ca(2+)-dependent cysteine proteases, calpains, regulate cell migration, cell death, insulin secretion, synaptic function and muscle homeostasis. Their endogenous inhibitor, calpastatin, consists of four inhibitory repeats, each of which neutralizes an activated calpain with exquisite specificity and potency. Despite the physiological importance of this interaction, the structural basis of calpain inhibition by calpastatin is unknown. Here we report the 3.0 A structure of Ca(2+)-bound m-calpain in complex with the first calpastatin repeat, both from rat, revealing the mechanism of exclusive specificity. The structure highlights the complexity of calpain activation by Ca(2+), illustrating key residues in a peripheral domain that serve to stabilize the protease core on Ca(2+) binding. Fully activated calpain binds ten Ca(2+) atoms, resulting in several conformational changes allowing recognition by calpastatin. Calpain inhibition is mediated by the intimate contact with three critical regions of calpastatin. Two regions target the penta-EF-hand domains of calpain and the third occupies the substrate-binding cleft, projecting a loop around the active site thiol to evade proteolysis.


    Related Citations: 
    • A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor
      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.
      (2003) J.Mol.Biol. 328: 131
    • The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium
      Hosfield, C.M.,Elce, J.S.,Davies, P.L.,Jia, Z.
      (2000) Proc.Natl.Acad.Sci.USA 97: 588
    • Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops gating the active site
      Moldoveanu, T.,Campbell, R.L.,Cuerrier, D.,Davies, P.L.
      (2004) J.Mol.Biol. 343: 1313
    • A Ca(2+) switch aligns the active site of calpain
      Moldoveanu, T.,Hosfield, C.M.,Lim, D.,Elce, J.S.,Jia, Z.,Davies, P.L.
      (2002) Cell 108: 649
    • Crystal structure of calpain reveals the structural basis for Ca(2+)-dependent protease activity and a novel mode of enzyme activation
      Todd, B.,Moore, D.,Deivanayagam, C.C.,Lin, G.D.,Chattopadhyay, D.,Maki, M.,Wang, K.K.,Narayana, S.V.
      (1999) Embo J. 18: 6880
    • Calpain silencing by a reversible intrinsic mechanism
      Moldoveanu, T.,Hosfield, C.M.,Lim, D.,Jia, Z.,Davies, P.L.
      (2003) Nat.Struct.Mol.Biol. 10: 371


    Organizational Affiliation

    Department of Immunology, St Jude Children's Research Hospital, 332 N Lauderdale, Memphis, Tennessee 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calpain-2 catalytic subunit
A
714Rattus norvegicusMutation(s): 1 
Gene Names: Capn2
EC: 3.4.22.53
Find proteins for Q07009 (Rattus norvegicus)
Go to UniProtKB:  Q07009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calpain small subunit 1
B
184Rattus norvegicusMutation(s): 0 
Gene Names: Capns1 (Capn4, Css1)
Find proteins for Q64537 (Rattus norvegicus)
Go to UniProtKB:  Q64537
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Calpastatin
C
86Rattus norvegicusMutation(s): 0 
Gene Names: Cast
Find proteins for P27321 (Rattus norvegicus)
Go to UniProtKB:  P27321
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.229 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 147.390α = 90.00
b = 147.390β = 90.00
c = 47.222γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references