8J6K

Crystal structure of pro-interleukin-18 and caspase-4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition and maturation of IL-18 by caspase-4 noncanonical inflammasome.

Shi, X.Sun, Q.Hou, Y.Zeng, H.Cao, Y.Dong, M.Ding, J.Shao, F.

(2023) Nature 624: 442-450

  • DOI: https://doi.org/10.1038/s41586-023-06742-w
  • Primary Citation of Related Structures:  
    8J6K

  • PubMed Abstract: 

    The canonical (caspase-1) and noncanonical (comprising caspases 4, 5 and 11; hereafter, caspase-4/5/11) inflammasomes both cleave gasdermin D (GSDMD) to induce pyroptosis 1,2 . Whereas caspase-1 processes IL-1β and IL-18 for maturation 3-6 , no cytokine target has been firmly established for lipopolysaccharide-activated caspase-4/5/11 7-9 . Here we show that activated human caspase-4, but not mouse caspase-11, directly and efficiently processes IL-18 in vitro and during bacterial infections. Caspase-4 cleaves the same tetrapeptide site in pro-IL-18 as caspase-1. The crystal structure of the caspase-4-pro-IL-18 complex reveals a two-site (binary) substrate-recognition mechanism; the catalytic pocket engages the tetrapeptide, and a unique exosite that critically recognizes GSDMD 10 similarly binds to a specific structure formed jointly by the propeptide and post-cleavage-site sequences in pro-IL-18. This binary recognition is also used by caspase-5 as well as caspase-1 to process pro-IL-18. In caspase-11, a structural deviation around the exosite underlies its inability to target pro-IL-18, which is restored by rationally designed mutations. The structure of pro-IL-18 features autoinhibitory interactions between the propeptide and the post-cleavage-site region, preventing recognition by the IL-18Rα receptor. Cleavage by caspase-1, -4 or -5 induces substantial conformational changes of IL-18 to generate two critical receptor-binding sites. Our study establishes IL-18 as a target of lipopolysaccharide-activated caspase-4/5. The finding is paradigm shifting in the understanding of noncanonical-inflammasome-mediated defences and also the function of IL-18 in immunity and disease.


  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing, Beijing, P. R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4 subunit p20169Homo sapiensMutation(s): 1 
Gene Names: CASP4ICH2
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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UniProt GroupP49662
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4 subunit p10B [auth a]88Homo sapiensMutation(s): 0 
Gene Names: CASP4ICH2
EC: 3.4.22.57
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Find proteins for P49662 (Homo sapiens)
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Go to UniProtKB:  P49662
PHAROS:  P49662
GTEx:  ENSG00000196954 
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UniProt GroupP49662
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-18C [auth B]194Homo sapiensMutation(s): 0 
Gene Names: IL18IGIFIL1F4
UniProt & NIH Common Fund Data Resources
Find proteins for Q14116 (Homo sapiens)
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PHAROS:  Q14116
GTEx:  ENSG00000150782 
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UniProt GroupQ14116
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine ADP-riboxanase OspC3D [auth C]161Shigella flexneriMutation(s): 0 
Gene Names: ospC3SF_p0115
EC: 4.3.99
UniProt
Find proteins for A0A0H2US87 (Shigella flexneri)
Explore A0A0H2US87 
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UniProt GroupA0A0H2US87
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.254α = 90
b = 86.254β = 90
c = 194.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Database references