8URV | pdb_00008urv

Solution NMR structure of pro-IL-18

• PDB DOI: https://doi.org/10.2210/pdb8URV/pdb
• BMRB: 31122

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-26 Released: 2024-05-29 
• Deposition Author(s): Bonin, J.P., Aramini, J.M., Kay, L.E.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural transitions enable interleukin-18 maturation and signaling.

Dong, Y., Bonin, J.P., Devant, P., Liang, Z., Sever, A.I.M., Mintseris, J., Aramini, J.M., Du, G., Gygi, S.P., Kagan, J.C., Kay, L.E., Wu, H.

(2024) Immunity 57: 1533

• PubMed: 38733997 
• DOI: https://doi.org/10.1016/j.immuni.2024.04.015
• Primary Citation Related Structures: 
  8SV1, 8URV


• PubMed Abstract: 
  

  Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron microscopy (cryo-EM), two major conformations of the complex between caspase-1 and pro-IL-18. One conformation is similar to the complex of caspase-4 and pro-IL-18, with interactions at both the active site and an exosite (closed conformation), and the other only contains interactions at the active site (open conformation). Thus, pro-IL-18 recruitment and processing by caspase-1 is less dependent on the exosite than the active site, unlike caspase-4. Structure determination by nuclear magnetic resonance uncovers a compact fold of apo pro-IL-18, which is similar to caspase-1-bound pro-IL-18 but distinct from cleaved IL-18. Binding sites for IL-18 receptor and IL-18 binding protein are only formed upon conformational changes after pro-IL-18 cleavage. These studies show how pro-IL-18 is selected as a caspase-1 substrate, and why cleavage is necessary for its inflammatory activity.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
Bioscience and Biomedical Engineering Thrust, Brain and Intelligence Research Institute, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China.
Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA.
Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: [e-mail].
Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada. Electronic address: [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 22.35 kDa 
• Atom Count: 1,562 
• Modeled Residue Count: 193 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-18	A	193	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Bonin, J.P., Aramini, J.M., Kay, L.E.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Database references