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- PDB-8j6k: Crystal structure of pro-interleukin-18 and caspase-4 complex -

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Basic information

Entry
Database: PDB / ID: 8j6k
TitleCrystal structure of pro-interleukin-18 and caspase-4 complex
Components
  • Arginine ADP-riboxanase OspC3
  • Caspase-4 subunit p10
  • Caspase-4 subunit p20
  • Interleukin-18
KeywordsHYDROLASE/IMMUNE SYSTEM / Inflammatory cytokine / Enzyme / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / interleukin-18 receptor binding / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death ...: / symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / interleukin-18 receptor binding / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death / non-canonical inflammasome complex assembly / symbiont-mediated perturbation of host programmed cell death / Interleukin-18 signaling / NLRP1 inflammasome complex / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / CARD domain binding / 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 / positive regulation of NK T cell proliferation / 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 / triglyceride homeostasis / T-helper 1 type immune response / positive regulation of tyrosine phosphorylation of STAT protein / natural killer cell mediated cytotoxicity / pyroptotic inflammatory response / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / intrinsic apoptotic signaling pathway / cholesterol homeostasis / protein maturation / cytokine activity / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction / : / NOD1/2 Signaling Pathway / positive regulation of type II interferon production / cellular response to amyloid-beta / cytokine-mediated signaling pathway / positive regulation of inflammatory response / cell-cell signaling / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / toxin activity / regulation of inflammatory response / angiogenesis / Interleukin-4 and Interleukin-13 signaling / host cell cytoplasm / calmodulin binding / cell population proliferation / 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 / innate immune response / cysteine-type endopeptidase activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / proteolysis / extracellular space / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Caspase recruitment domain / Cytokine IL1/FGF / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / 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
Arginine ADP-riboxanase OspC3 / Caspase-4 / Interleukin-18
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsSun, Q. / Hou, Y.J. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nature / Year: 2023
Title: Recognition and maturation of IL-18 by caspase-4 noncanonical inflammasome.
Authors: Shi, X. / Sun, Q. / Hou, Y. / Zeng, H. / Cao, Y. / Dong, M. / Ding, J. / Shao, F.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-4 subunit p20
a: Caspase-4 subunit p10
B: Interleukin-18
C: Arginine ADP-riboxanase OspC3


Theoretical massNumber of molelcules
Total (without water)70,5584
Polymers70,5584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.254, 86.254, 194.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Caspase-4 subunit p20


Mass: 19330.045 Da / Num. of mol.: 1 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662
#2: Protein Caspase-4 subunit p10 / CASP-4 / ICE and Ced-3 homolog 2 / ICH-2 / ICE(rel)-II / Mih1 / Protease TX


Mass: 10423.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662, caspase-4
#3: Protein Interleukin-18 / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 ...IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma


Mass: 22437.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18, IGIF, IL1F4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14116
#4: Protein Arginine ADP-riboxanase OspC3


Mass: 18366.213 Da / Num. of mol.: 1 / Fragment: ARD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3, SF_p0115 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H2US87, Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium acetate, 0.1M Tris-HCl pH 9.0, 13% PEG 8000, 0.01 M L-Glutathione reduced, 0.01 M L-Glutathione oxidized

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.12→74.7 Å / Num. obs: 15561 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 101.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Rrim(I) all: 0.119 / Net I/σ(I): 16
Reflection shellResolution: 3.12→3.29 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.312 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2223 / CC1/2: 0.71 / Rpim(I) all: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→59.2 Å / SU ML: 0.514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 1551 10.01 %
Rwork0.2378 13946 -
obs0.2411 15497 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.01 Å2
Refinement stepCycle: LAST / Resolution: 3.12→59.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4269 0 0 0 4269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384341
X-RAY DIFFRACTIONf_angle_d0.55035826
X-RAY DIFFRACTIONf_chiral_restr0.044645
X-RAY DIFFRACTIONf_plane_restr0.0038743
X-RAY DIFFRACTIONf_dihedral_angle_d12.33271648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.220.35781370.32961248X-RAY DIFFRACTION100
3.22-3.340.31981390.29471244X-RAY DIFFRACTION100
3.34-3.470.32681420.30481240X-RAY DIFFRACTION100
3.47-3.630.32431360.27141250X-RAY DIFFRACTION100
3.63-3.820.30861360.27051236X-RAY DIFFRACTION99.93
3.82-4.060.32851410.25491258X-RAY DIFFRACTION100
4.06-4.370.27221380.22611271X-RAY DIFFRACTION100
4.37-4.810.24271400.21331266X-RAY DIFFRACTION99.86
4.81-5.510.26651470.23411265X-RAY DIFFRACTION100
5.51-6.930.29371430.25491307X-RAY DIFFRACTION100
6.94-59.20.20951520.20171361X-RAY DIFFRACTION98.7

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