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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-1Caspase 1) x 2
  • Interleukin-18Interleukin 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 / positive regulation of tissue remodeling / The IPAF inflammasome ...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 / positive regulation of tissue remodeling / The IPAF inflammasome / NLRP1 inflammasome complex / icosanoid biosynthetic process / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / positive regulation of macrophage derived foam cell differentiation / caspase binding / neutrophil activation / CARD domain binding / osmosensory signaling pathway / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / sleep / natural killer cell activation / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / positive regulation of NK T cell proliferation / Interleukin-37 signaling / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor signaling pathway / T-helper 1 type immune response / cellular response to organic substance / positive regulation of interleukin-13 production / positive regulation of activated T cell proliferation / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / positive regulation of interleukin-17 production / Interleukin-10 signaling / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of natural killer cell proliferation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein maturation / The NLRP3 inflammasome / protein autoprocessing / establishment of skin barrier / Pyroptosis / Purinergic signaling in leishmaniasis infection / regulation of cell adhesion / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cholesterol homeostasis / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of smooth muscle cell proliferation / NOD1/2 Signaling Pathway / kinase binding / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / angiogenesis / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / cellular response to lipopolysaccharide / cell population proliferation / microtubule / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / defense response to bacterium / 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 family C14A, His active site / Caspase family histidine 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 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: To Be Published
Title: Caspase-1 complex with interleukin-18
Authors: Pascal, D. / Dong, Y. / Wu, H. / Jon, K.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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
Water0
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 / 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 / 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 / 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

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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 FIELDBright-field microscopy / 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

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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