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- EMDB-3241: Cryo-EM reconstruction of caspase-1 CARD -

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Basic information

Entry
Database: EMDB / ID: EMD-3241
TitleCryo-EM reconstruction of caspase-1 CARD
Map dataReconstruction of caspase-1 CARD filament
Sample
  • Sample: Human caspase-1 CARD
  • Protein or peptide: Caspase-1 CARD
KeywordsCaspase-1 / CARD / inflammasome / filament / cryo-EM / signalosome / helical reconstruction / death domain
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / microtubule / defense response to virus / endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Caspase recruitment domain / 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. ...Caspase recruitment domain / 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
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi Y / Lu A / Schmidt FI / Yin Q / Chen S / Fu T-M / Tong AB / Ploegh HL / Mao Y / Wu H
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Molecular basis of caspase-1 polymerization and its inhibition by a new capping mechanism.
Authors: Alvin Lu / Yang Li / Florian I Schmidt / Qian Yin / Shuobing Chen / Tian-Min Fu / Alexander B Tong / Hidde L Ploegh / Youdong Mao / Hao Wu /
Abstract: Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions ...Inflammasomes are cytosolic caspase-1-activation complexes that sense intrinsic and extrinsic danger signals, and trigger inflammatory responses and pyroptotic cell death. Homotypic interactions among Pyrin domains and caspase recruitment domains (CARDs) in inflammasome-complex components mediate oligomerization into filamentous assemblies. Several cytosolic proteins consisting of only interaction domains exert inhibitory effects on inflammasome assembly. In this study, we determined the structure of the human caspase-1 CARD domain (caspase-1(CARD)) filament by cryo-electron microscopy and investigated the biophysical properties of two caspase-1-like CARD-only proteins: human inhibitor of CARD (INCA or CARD17) and ICEBERG (CARD18). Our results reveal that INCA caps caspase-1 filaments, thereby exerting potent inhibition with low-nanomolar Ki on caspase-1(CARD) polymerization in vitro and inflammasome activation in cells. Whereas caspase-1(CARD) uses six complementary surfaces of three types for filament assembly, INCA is defective in two of the six interfaces and thus terminates the caspase-1 filament.
History
DepositionNov 11, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseMar 30, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fna
  • Surface level: 3.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fna
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3241_tit...

Downloads & links

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Map

FileDownload / File: emd_3241.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of caspase-1 CARD filament
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 3.15 / Movie #1: 3.15
Minimum - Maximum-2.27765226 - 5.90264797
Average (Standard dev.)0.71799731 (±0.87744838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-79
Dimensions160160160
Spacing160160160
CellA=B=C: 139.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z139.200139.200139.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-79
NC/NR/NS160160160
D min/max/mean-2.2785.9030.718

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Supplemental data

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Sample components

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Entire : Human caspase-1 CARD

EntireName: Human caspase-1 CARD
Components
  • Sample: Human caspase-1 CARD
  • Protein or peptide: Caspase-1 CARD

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Supramolecule #1000: Human caspase-1 CARD

SupramoleculeName: Human caspase-1 CARD / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1

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Macromolecule #1: Caspase-1 CARD

MacromoleculeName: Caspase-1 CARD / type: protein_or_peptide / ID: 1 / Oligomeric state: Helical / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 DE3 / Recombinant plasmid: pDB-HIs-MBP
SequenceUniProtKB: Caspase-1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8 / Details: 20 mM Sodium HEPES, pH 8.0, 150 mM NaCl, 2 mM DTT
GridDetails: holey carbon C-flat grids (R1.2/1.3, Photochip, CA), glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: blotted for 3 seconds before plunging

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Electron microscopy

MicroscopeOTHER
DateFeb 2, 2015
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Number real images: 200 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 28736 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.006 µm / Nominal defocus min: 0.001 µm
Sample stageSpecimen holder model: OTHER

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Image processing

DetailsThe particles were aligned using IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: SPIDER, IHRSR
CTF correctionDetails: Each micrograph

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