1QDU

CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE KETONE INHIBITOR ZEVD-DCBMK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

The three-dimensional structure of caspase-8: an initiator enzyme in apoptosis.

Blanchard, H.Kodandapani, L.Mittl, P.R.Marco, S.D.Krebs, J.F.Wu, J.C.Tomaselli, K.J.Grutter, M.G.

(1999) Structure 7: 1125-1133

  • DOI: https://doi.org/10.1016/s0969-2126(99)80179-8
  • Primary Citation of Related Structures:  
    1QDU

  • PubMed Abstract: 

    In the initial stages of Fas-mediated apoptosis the cysteine protease caspase-8 is recruited to the cell receptor as a zymogen (procaspase-8) and is incorporated into the death-signalling complex. Procaspase-8 is subsequently activated leading to a cascade of proteolytic events, one of them being the activation of caspase-3, and ultimately resulting in cell destruction. Variations in the substrate specificity of different caspases have been reported. We report here the crystal structure of a complex of the activated human caspase-8 (proteolytic domain) with the irreversible peptidic inhibitor Z-Glu-Val-Asp-dichloromethylketone at 2.8 A resolution. This is the first structure of a representative of the long prodomain initiator caspases and of the group III substrate specificity class. The overall protein architecture resembles the caspase-1 and caspase-3 folds, but shows distinct structural differences in regions forming the active site. In particular, differences observed in subsites S(3), S(4) and the loops involved in inhibitor interactions explain the preference of caspase-8 for substrates with the sequence (Leu/Val)-Glu-X-Asp. The structural differences could be correlated with the observed substrate specificities of caspase-1, caspase-3 and caspase-8, as determined from kinetic experiments. This information will help us to understand the role of the various caspases in the propagation of the apoptotic signal. The information gained from this investigation should be useful for the design of specific inhibitors.


  • Organizational Affiliation

    Biochemisches Institut Universität Zürich Winterthurer Strasse 190, CH-8057, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CASPASE-8 ALPHA-CHAIN153Homo sapiensMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CASPASE-8 BETA-CHAIN88Homo sapiensMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PHQ-GLU-VAL-ASP-DICHLOROMETHYLKETONE INHIBITOR5N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.9α = 90
b = 206.53β = 102.3
c = 102.05γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.5: 2024-04-03
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-13
    Changes: Structure summary