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- EMDB-40781: Caspase-1 complex with interleukin-18 -

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ID or keywords:

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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 / aldose 1-epimerase activity / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / galactose catabolic process via UDP-galactose / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response ...interleukin-18 receptor binding / aldose 1-epimerase activity / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / galactose catabolic process via UDP-galactose / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / Interleukin-1 processing / negative regulation of myoblast differentiation / type 2 immune response / sleep / natural killer cell activation / positive regulation of NK T cell proliferation / triglyceride homeostasis / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / natural killer cell mediated cytotoxicity / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / cholesterol homeostasis / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / glucose metabolic process / cell-cell signaling / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / DNA damage response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Interleukin-18 / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
Uncharacterized protein YphB / 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: To Be Published
Title: Caspase-1 complex with interleukin-18
Authors: Pascal D / Dong Y / Wu H / Jon K
History
DepositionMay 15, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40781.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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Sample components

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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

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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

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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: Uncharacterized protein YphB

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Macromolecule #2: Caspase-1

MacromoleculeName: Caspase-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ec: 3.4.22.36
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: Uncharacterized protein YphB

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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

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Image processing

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

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