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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1016/j.cell.2020.02.002
  • Primary Citation of Related Structures:  
    6KN1, 6KMU, 6KMT, 6KMV, 6KN0, 6KMZ

  • 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 ...

    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: 

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China. Electronic address: jding@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-4A, B, D [auth C], E [auth D]185Homo sapiensMutation(s): 1 
Gene Names: CASP4, ICH2
EC: 3.4.22.57
UniProt & NIH Common Fund Data Resources
Find proteins for P49662 (Homo sapiens)
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Go to UniProtKB:  P49662
PHAROS:  P49662
GTEx:  ENSG00000196954
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gasdermin-DC [auth E]194Homo sapiensMutation(s): 0 
Gene Names: GSDMD, DFNA5L, GSDMDC1, FKSG10
UniProt & NIH Common Fund Data Resources
Find proteins for P57764 (Homo sapiens)
Explore P57764 
Go to UniProtKB:  P57764
PHAROS:  P57764
GTEx:  ENSG00000104518
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Gasdermin-DF [auth H]195Homo sapiensMutation(s): 0 
Gene Names: GSDMD, DFNA5L, GSDMDC1, FKSG10
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Find proteins for P57764 (Homo sapiens)
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PHAROS:  P57764
GTEx:  ENSG00000104518
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-4G [auth a], H [auth b], I [auth c], J [auth d]88Homo sapiensMutation(s): 0 
Gene Names: CASP4, ICH2
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
Protein Feature View
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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

  • Deposited Date: 2019-08-01 
  • Released Date: 2020-03-11 
    • Deposition Author(s): Ding, J., Sun, Q.

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