4JR1 | pdb_00004jr1

Human procaspase-7 bound to Ac-DEVD-CMK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4JR1

This is version 1.5 of the entry. See complete history

Literature

Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation.

Thomsen, N.D.Koerber, J.T.Wells, J.A.

(2013) Proc Natl Acad Sci U S A 110: 8477-8482

  • DOI: https://doi.org/10.1073/pnas.1306759110
  • Primary Citation Related Structures: 
    4JQY, 4JQZ, 4JR0, 4JR1, 4JR2

  • PubMed Abstract: 

    Procaspase-3 (P3) and procaspase-7 (P7) are activated through proteolytic maturation to form caspase-3 (C3) and caspase-7 (C7), respectively, which serve overlapping but nonredundant roles as the executioners of apoptosis in humans. However, it is unclear if differences in P3 and P7 maturation mechanisms underlie their unique biological functions, as the structure of P3 remains unknown. Here, we report structures of P3 in a catalytically inactive conformation, structures of P3 and P7 bound to covalent peptide inhibitors that reveal the active conformation of the zymogens, and the structure of a partially matured C7:P7 heterodimer. Along with a biochemical analysis, we show that P3 is catalytically inactive and matures through a symmetric all-or-nothing process. In contrast, P7 contains latent catalytic activity and matures through an asymmetric and tiered mechanism, suggesting a lower threshold for activation. Finally, we use our structures to design a selection strategy for conformation specific antibody fragments that stimulate procaspase activity, showing that executioner procaspase conformational equilibrium can be rationally modulated. Our studies provide a structural framework that may help to explain the unique roles of these important proapoptotic enzymes, and suggest general strategies for the discovery of proenzyme activators.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.

Macromolecule Content 

  • Total Structure Weight: 57.78 kDa 
  • Atom Count: 3,887 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 512 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Procaspase-7
A, B
250Homo sapiensMutation(s): 1 
Gene Names: CASP7MCH3
EC: 3.4.22.60
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
PHAROS:  P55210
GTEx:  ENSG00000165806 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55210
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ac-DEVD-CMK
C, D
6N/AMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AKZ
Query on AKZ
C, D
PEPTIDE-LIKEC4 H9 N O4ASP

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.284α = 90
b = 100.016β = 90
c = 161.587γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ELVESrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2013-06-05
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-27
    Changes: Structure summary