8SPB | pdb_00008spb

Caspase-4/Pro-IL-18 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.3 of the entry. See complete history

Literature

Structural insights into cytokine cleavage by inflammatory caspase-4.

Devant, P.Dong, Y.Mintseris, J.Ma, W.Gygi, S.P.Wu, H.Kagan, J.C.

(2023) Nature 624: 451-459

  • DOI: https://doi.org/10.1038/s41586-023-06751-9
  • Primary Citation Related Structures: 
    8SPB

  • PubMed Abstract: 

    Inflammatory caspases are key enzymes in mammalian innate immunity that control the processing and release of interleukin-1 (IL-1)-family cytokines 1,2 . Despite the biological importance, the structural basis for inflammatory caspase-mediated cytokine processing has remained unclear. To date, catalytic cleavage of IL-1-family members, including pro-IL-1β and pro-IL-18, has been attributed primarily to caspase-1 activities within canonical inflammasomes 3 . Here we demonstrate that the lipopolysaccharide receptor caspase-4 from humans and other mammalian species (except rodents) can cleave pro-IL-18 with an efficiency similar to pro-IL-1β and pro-IL-18 cleavage by the prototypical IL-1-converting enzyme caspase-1. This ability of caspase-4 to cleave pro-IL-18, combined with its previously defined ability to cleave and activate the lytic pore-forming protein gasdermin D (GSDMD) 4,5 , enables human cells to bypass the need for canonical inflammasomes and caspase-1 for IL-18 release. The structure of the caspase-4-pro-IL-18 complex determined using cryogenic electron microscopy reveals that pro-lL-18 interacts with caspase-4 through two distinct interfaces: a protease exosite and an interface at the caspase-4 active site involving residues in the pro-domain of pro-IL-18, including the tetrapeptide caspase-recognition sequence 6 . The mechanisms revealed for cytokine substrate capture and cleavage differ from those observed for the caspase substrate GSDMD 7,8 . These findings provide a structural framework for the discussion of caspase activities in health and disease.


  • Organizational Affiliation
    • Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 111.95 kDa 
  • Atom Count: 6,726 
  • Modeled Residue Count: 828 
  • Deposited Residue Count: 974 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-4 subunit p20A,
D [auth a]
207Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-4 subunit p10B,
E [auth b]
92Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-18C,
F [auth c]
188Homo sapiensMutation(s): 0 
Gene Names: IL18
UniProt & NIH Common Fund Data Resources
Find proteins for Q14116 (Homo sapiens)
Explore Q14116 
Go to UniProtKB:  Q14116
PHAROS:  Q14116
GTEx:  ENSG00000150782 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14116
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 2.0: 2023-11-29
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-12-06
    Changes: Database references
  • Version 2.2: 2023-12-27
    Changes: Database references
  • Version 2.3: 2025-05-21
    Changes: Data collection, Structure summary