+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40781 | |||||||||
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Title | Caspase-1 complex with interleukin-18 | |||||||||
Map data | caspase-1 in complex with interleukin-18Caspase 1 | |||||||||
Sample |
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Keywords | Innate 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 / 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 / caspase binding / positive regulation of macrophage derived foam cell differentiation / 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 / protein autoprocessing / The NLRP3 inflammasome / 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 / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / 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 / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / defense response to virus / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Dong Y / Pascal D / Jon K / Wu H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Caspase-1 complex with interleukin-18 Authors: Pascal D / Dong Y / Wu H / Jon K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40781.map.gz | 68.3 MB | EMDB map data format | |
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Header (meta data) | emd-40781-v30.xml emd-40781.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_40781.png | 37.5 KB | ||
Filedesc metadata | emd-40781.cif.gz | 5.4 KB | ||
Others | emd_40781_half_map_1.map.gz emd_40781_half_map_2.map.gz | 68.4 MB 68.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40781 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40781 | HTTPS FTP |
-Related structure data
Related structure data | 8sv1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40781.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | caspase-1 in complex with interleukin-18 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: caspase-1 in complex with interleukin-18 half map A
File | emd_40781_half_map_1.map | ||||||||||||
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Annotation | caspase-1 in complex with interleukin-18 half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: caspase-1 in complex with interleukin-18 half map B
File | emd_40781_half_map_2.map | ||||||||||||
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Annotation | caspase-1 in complex with interleukin-18 half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : protein complex with interleukin
Entire | Name: protein complex with interleukin |
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Components |
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-Supramolecule #1: protein complex with interleukin
Supramolecule | Name: protein complex with interleukin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 100 MDa |
-Macromolecule #1: Caspase-1
Macromolecule | Name: Caspase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.607154 KDa |
Recombinant expression | Organism: Escherichia coli B (bacteria) |
Sequence | String: AEIYPIMDKS SRTRLALIIC NEEFDSIPRR TGAEVDITGM TMLLQNLGYS VDVKKNLTAS DMTTELEAFA HRPEHKTSDS TFLVFMSHG IREGICGKKH SEQVPDILQL NAIFNMLNTK NCPSLKDKPK VIIIQACRGD SPGVVWFKD UniProtKB: Caspase-1 |
-Macromolecule #2: Caspase-1
Macromolecule | Name: Caspase-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.258755 KDa |
Recombinant expression | Organism: Escherichia coli B (bacteria) |
Sequence | String: AIKKAHIEKD FIAFCSSTPD NVSWRHPTMG SVFIGRLIEH MQEYACSCDV EEIFRKVRFS FEQPDGRAQM PTTERVTLTR CFYLFPGH UniProtKB: Caspase-1 |
-Macromolecule #3: Interleukin-18
Macromolecule | Name: Interleukin-18 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.850641 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: 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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260549 |