6KMZ

caspase-4 P22/P10 C258A in complex with human GSDMD-C domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.311 
  • R-Value Observed: 0.312 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6KMT


Literature

Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis.

Wang, K.Sun, Q.Zhong, X.Zeng, M.Zeng, H.Shi, X.Li, Z.Wang, Y.Zhao, Q.Shao, F.Ding, J.

(2020) Cell 180: 941

  • DOI: https://doi.org/10.1016/j.cell.2020.02.002
  • Primary Citation of Related Structures:  
    6KMT, 6KMU, 6KMV, 6KMZ, 6KN0, 6KN1

  • PubMed Abstract: 

    The pyroptosis execution protein GSDMD is cleaved by inflammasome-activated caspase-1 and LPS-activated caspase-11/4/5. The cleavage unmasks the pore-forming domain from GSDMD-C-terminal domain. How the caspases recognize GSDMD and its connection with caspase activation are unknown. Here, we show site-specific caspase-4/11 autoprocessing, generating a p10 product, is required and sufficient for cleaving GSDMD and inducing pyroptosis. The p10-form autoprocessed caspase-4/11 binds the GSDMD-C domain with a high affinity. Structural comparison of autoprocessed and unprocessed capase-11 identifies a β sheet induced by the autoprocessing. In caspase-4/11-GSDMD-C complex crystal structures, the β sheet organizes a hydrophobic GSDMD-binding interface that is only possible for p10-form caspase-4/11. The binding promotes dimerization-mediated caspase activation, rendering a cleavage independently of the cleavage-site tetrapeptide sequence. Crystal structure of caspase-1-GSDMD-C complex shows a similar GSDMD-recognition mode. Our study reveals an unprecedented substrate-targeting mechanism for caspases. The hydrophobic interface suggests an additional space for developing inhibitors specific for pyroptotic caspases.


  • Organizational Affiliation

    Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4A,
B,
D [auth C],
E [auth D]
185Homo sapiensMutation(s): 1 
Gene Names: CASP4ICH2
EC: 3.4.22.57
UniProt & NIH Common Fund Data Resources
Find proteins for P49662 (Homo sapiens)
Explore P49662 
Go to UniProtKB:  P49662
PHAROS:  P49662
GTEx:  ENSG00000196954 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49662
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-DC [auth E]194Homo sapiensMutation(s): 0 
Gene Names: GSDMDDFNA5LGSDMDC1FKSG10
UniProt & NIH Common Fund Data Resources
Find proteins for P57764 (Homo sapiens)
Explore P57764 
Go to UniProtKB:  P57764
PHAROS:  P57764
GTEx:  ENSG00000104518 
Entity Groups  
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UniProt GroupP57764
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-DF [auth H]195Homo sapiensMutation(s): 0 
Gene Names: GSDMDDFNA5LGSDMDC1FKSG10
UniProt & NIH Common Fund Data Resources
Find proteins for P57764 (Homo sapiens)
Explore P57764 
Go to UniProtKB:  P57764
PHAROS:  P57764
GTEx:  ENSG00000104518 
Entity Groups  
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UniProt GroupP57764
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4G [auth a],
H [auth b],
I [auth c],
J [auth d]
88Homo sapiensMutation(s): 0 
Gene Names: CASP4ICH2
EC: 3.4.22.57
UniProt & NIH Common Fund Data Resources
Find proteins for P49662 (Homo sapiens)
Explore P49662 
Go to UniProtKB:  P49662
PHAROS:  P49662
GTEx:  ENSG00000196954 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49662
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.311 
  • R-Value Observed: 0.312 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.568α = 90
b = 140.568β = 90
c = 329.355γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description