8J6K | pdb_00008j6k

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

• PDB DOI: https://doi.org/10.2210/pdb8J6K/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-26 Released: 2023-11-29 
• Deposition Author(s): Sun, Q., Hou, Y.J., Ding, J.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Models: experimental

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

• PubMed: 37993714 
• DOI: https://doi.org/10.1038/s41586-023-06742-w
• Primary Citation 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.

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Organizational Affiliation: 
• National Institute of Biological Sciences, Beijing, Beijing, P. R. China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China.
University of Chinese Academy of Sciences, Beijing, P. R. China.
National Institute of Biological Sciences, Beijing, Beijing, P. R. China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
University of Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
National Institute of Biological Sciences, Beijing, Beijing, P. R. China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P. R. China. [e-mail].
Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, Beijing, P. R. China. [e-mail].
Changping Laboratory, Beijing, P. R. China. [e-mail].
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, P. R. China. [e-mail].
New Cornerstone Science Laboratory, Shenzhen, P. R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.56 kDa 
• Atom Count: 4,269 
• Modeled Residue Count: 526 
• Deposited Residue Count: 612 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-4 subunit p20	A	169	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-4 subunit p10	B [auth a]	88	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-18	C [auth B]	194	Homo sapiens	Mutation(s): 0  Gene Names: IL18, IGIF, IL1F4
UniProt & NIH Common Fund Data Resources
Find proteins for Q14116 (Homo sapiens) Explore Q14116  Go to UniProtKB:  Q14116
PHAROS:  Q14116 GTEx:  ENSG00000150782

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine ADP-riboxanase OspC3	D [auth C]	161	Shigella flexneri	Mutation(s): 0  Gene Names: ospC3, SF_p0115 EC: 4.3.99
UniProt
Find proteins for A0A0H2US87 (Shigella flexneri) Explore A0A0H2US87  Go to UniProtKB:  A0A0H2US87

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.254	α = 90
b = 86.254	β = 90
c = 194.12	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Sun, Q., Hou, Y.J., Ding, J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• 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