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 
  • R-Value Observed: 0.232 

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
  • Structures With Same Primary Citation

  • 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 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
    • 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
    • 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
    • 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 U S A 97: 588
    • 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
    • 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

    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 subunitA714Rattus norvegicusMutation(s): 1 
Gene Names: Capn2
EC: 3.4.22.53
Find proteins for Q07009 (Rattus norvegicus)
Explore Q07009 
Go to UniProtKB:  Q07009
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calpain small subunit 1B184Rattus norvegicusMutation(s): 1 
Gene Names: Capns1Capn4Css1
Find proteins for Q64537 (Rattus norvegicus)
Explore Q64537 
Go to UniProtKB:  Q64537
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CalpastatinC86Rattus norvegicusMutation(s): 0 
Gene Names: Cast
Find proteins for P27321 (Rattus norvegicus)
Explore P27321 
Go to UniProtKB:  P27321
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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 
  • R-Value Observed: 0.232 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.39α = 90
b = 147.39β = 90
c = 47.222γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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