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- PDB-8sv1: Caspase-1 complex with interleukin-18 -

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Basic information

Entry
Database: PDB / ID: 8sv1
TitleCaspase-1 complex with interleukin-18
Components
  • (Caspase-1) x 2
  • Interleukin-18
KeywordsHYDROLASE / IMMUNE SYSTEM / Innate immune / Complex
Function / homology
Function and homology information


interleukin-18 receptor binding / caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / Interleukin-18 signaling / The IPAF inflammasome / icosanoid biosynthetic process ...interleukin-18 receptor binding / caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / Interleukin-18 signaling / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / positive regulation of tissue remodeling / canonical inflammasome complex / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of interleukin-18 production / CARD domain binding / cytokine precursor processing / NLRP3 inflammasome complex / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation / negative regulation of myoblast differentiation / Interleukin-1 processing / osmosensory signaling pathway / positive regulation of NK T cell proliferation / Interleukin-37 signaling / sleep / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage derived foam cell differentiation / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / triglyceride homeostasis / T-helper 1 type immune response / positive regulation of tyrosine phosphorylation of STAT protein / signaling receptor ligand precursor processing / natural killer cell mediated cytotoxicity / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cytokine binding / Interleukin-10 signaling / positive regulation of interleukin-17 production / positive regulation of natural killer cell proliferation / protein autoprocessing / positive regulation of activated T cell proliferation / The NLRP3 inflammasome / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of smooth muscle cell proliferation / cholesterol homeostasis / protein maturation / cytokine activity / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / : / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / cell-cell signaling / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / regulation of inflammatory response / angiogenesis / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / endopeptidase activity / defense response to virus / microtubule / cell population proliferation / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / defense response to bacterium / immune response / inflammatory response / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Caspase recruitment domain / Cytokine IL1/FGF / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site ...Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Caspase recruitment domain / Cytokine IL1/FGF / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Caspase-1 / Interleukin-18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDong, Y. / Pascal, D. / Jon, K. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2024
Title: Structural transitions enable interleukin-18 maturation and signaling.
Authors: Ying Dong / Jeffrey P Bonin / Pascal Devant / Zhuoyi Liang / Alexander I M Sever / Julian Mintseris / James M Aramini / Gang Du / Stephen P Gygi / Jonathan C Kagan / Lewis E Kay / Hao Wu /
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 ...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.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0May 8, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 8, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
a: Caspase-1
b: Caspase-1
C: Interleukin-18
c: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)97,4336
Polymers97,4336
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Caspase-1


Mass: 16607.154 Da / Num. of mol.: 2 / Fragment: subunit P20 (UNP residues 120-297)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1 / Production host: Escherichia coli B (bacteria) / References: UniProt: P29466
#2: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 10258.755 Da / Num. of mol.: 2 / Fragment: subunit P10 (UNP residues 317-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli B (bacteria) / References: UniProt: P29466, caspase-1
#3: Protein Interleukin-18


Mass: 21850.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18 / Plasmid: pFastBac1-HM / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q14116
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: protein complex with interleukin / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 100 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 260549 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036472
ELECTRON MICROSCOPYf_angle_d0.4438706
ELECTRON MICROSCOPYf_dihedral_angle_d4.074840
ELECTRON MICROSCOPYf_chiral_restr0.042964
ELECTRON MICROSCOPYf_plane_restr0.0031124

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