[English] 日本語
Yorodumi
- EMDB-40781: Caspase-1 complex with interleukin-18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40781
TitleCaspase-1 complex with interleukin-18
Map datacaspase-1 in complex with interleukin-18
Sample
  • Complex: protein complex with interleukin
    • Protein or peptide: Caspase-1
    • Protein or peptide: Caspase-1
    • Protein or peptide: Interleukin-18
KeywordsInnate immune / Complex / HYDROLASE / IMMUNE SYSTEM
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 / positive regulation of tissue remodeling / NLRP1 inflammasome complex / canonical inflammasome complex / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / cytokine precursor processing / positive regulation of interleukin-18 production / CARD domain binding / NLRP3 inflammasome complex / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation / positive regulation of NK T cell proliferation / negative regulation of myoblast differentiation / osmosensory signaling pathway / Interleukin-1 processing / positive regulation of natural killer cell proliferation / positive regulation of tumor necrosis factor-mediated signaling pathway / sleep / Interleukin-37 signaling / positive regulation of macrophage derived foam cell differentiation / triglyceride homeostasis / 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 / positive regulation of tyrosine phosphorylation of STAT protein / T-helper 1 type immune response / natural killer cell mediated cytotoxicity / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / Interleukin-10 signaling / cytokine binding / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / protein autoprocessing / The NLRP3 inflammasome / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / protein maturation / cholesterol homeostasis / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / NOD1/2 Signaling Pathway / cytokine-mediated signaling pathway / cellular response to type II interferon / kinase binding / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / 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 / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / angiogenesis / endopeptidase activity / defense response to virus / microtubule / positive regulation of canonical NF-kappaB signal transduction / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDong Y / Pascal D / Jon K / Wu H
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40781.png

Downloads & links

-
Map

FileDownload / File: emd_40781.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcaspase-1 in complex with interleukin-18
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 268 pix.
= 222.44 Å		0.83 Å/pix.
x 268 pix.
= 222.44 Å		0.83 Å/pix.
x 268 pix.
= 222.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-2.751015 - 3.887464
Average (Standard dev.)-0.00000000000039 (±0.06845663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions268268268
Spacing268268268
CellA=B=C: 222.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: caspase-1 in complex with interleukin-18 half map A

Fileemd_40781_half_map_1.map
Annotationcaspase-1 in complex with interleukin-18 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: caspase-1 in complex with interleukin-18 half map B

Fileemd_40781_half_map_2.map
Annotationcaspase-1 in complex with interleukin-18 half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : protein complex with interleukin

EntireName: protein complex with interleukin
Components
  • Complex: protein complex with interleukin
    • Protein or peptide: Caspase-1
    • Protein or peptide: Caspase-1
    • Protein or peptide: Interleukin-18

-
Supramolecule #1: protein complex with interleukin

SupramoleculeName: protein complex with interleukin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 MDa

-
Macromolecule #1: Caspase-1

MacromoleculeName: Caspase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.607154 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString:
AEIYPIMDKS SRTRLALIIC NEEFDSIPRR TGAEVDITGM TMLLQNLGYS VDVKKNLTAS DMTTELEAFA HRPEHKTSDS TFLVFMSHG IREGICGKKH SEQVPDILQL NAIFNMLNTK NCPSLKDKPK VIIIQACRGD SPGVVWFKD

UniProtKB: Caspase-1

-
Macromolecule #2: Caspase-1

MacromoleculeName: Caspase-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.258755 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString:
AIKKAHIEKD FIAFCSSTPD NVSWRHPTMG SVFIGRLIEH MQEYACSCDV EEIFRKVRFS FEQPDGRAQM PTTERVTLTR CFYLFPGH

UniProtKB: Caspase-1

-
Macromolecule #3: Interleukin-18

MacromoleculeName: Interleukin-18 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.850641 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
VEDNCINFVA MKFIDNTLYF IAEDDENLES DYFGKLESKL SVIRNLNDQV LFIDQGNRPL FEDMTDSDCR DNAPRTIFII SMYKDSQPR GMAVTISVKC EKISTLSCEN KIISFKEMNP PDNIKDTKSD IIFFQRSVPG HDNKMQFESS SYEGYFLACE K ERDLFKLI LKKEDELGDR SIMFTVQNED

UniProtKB: Interleukin-18

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nry

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260549
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more