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- EMDB-66403: Full-length Caspase-1-CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-66403
TitleFull-length Caspase-1-CARD filament
Map data
Sample
  • Cell: Filament
    • Protein or peptide: Caspase-1
Keywordsfilament / PYD / CARD / IMMUNE SYSTEM
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex / positive regulation of interleukin-18 production / CARD domain binding / cytokine precursor processing / NLRP3 inflammasome complex / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / positive regulation of tumor necrosis factor-mediated signaling pathway / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / cytokine binding / pyroptotic inflammatory response / protein autoprocessing / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / protein maturation / positive regulation of interleukin-1 beta production / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / cellular response to lipopolysaccharide / regulation of inflammatory response / regulation of apoptotic process / endopeptidase activity / defense response to virus / microtubule / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / 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 recruitment domain / 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
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsXue D / Ni F / Liu S / Yan H / Luo Z / Fu G / Wang Q / Ma J
Funding support China, 3 items
OrganizationGrant numberCountry
Other governmentNational Key Research and Development Program of China (No. 2024YFA1307502) China
Other governmentScience and Technology Innovation Plan of Shanghai Science and Technology Commission (No. 23JS1400200) China
Other governmentResearch Fund for International Senior Scientists (No. W2431060) China
CitationJournal: Nat Commun / Year: 2025
Title: Atomic mechanisms of full-length ASC-mediated inflammasome assembly.
Authors: Dongmei Xue / Fengyun Ni / Sheng Liu / Huifang Yan / Zhenwei Luo / Gang Fu / Qinghua Wang / Jianpeng Ma /
Abstract: ASC (Apoptosis-associated Speck-like protein containing a CARD) is a key adaptor protein that assembles inflammasomes by linking sensors such as NLRP3 to effectors like Caspase-1 via its PYD and CARD ...ASC (Apoptosis-associated Speck-like protein containing a CARD) is a key adaptor protein that assembles inflammasomes by linking sensors such as NLRP3 to effectors like Caspase-1 via its PYD and CARD Death Domains. Due to ASC's propensity to self-aggregate, most high-resolution structural studies focused on isolated PYD or CARD domains, leaving the atomic basis of full-length ASC assembly unknown. Here we determine atomic-resolution cryo-EM structures of PYD and CARD filaments from full-length ASC, revealing characteristic multitrack bundles composed of alternating ASC and ASC filaments that expose multiple interfaces for flexible assembly and efficient signaling. We further show that Caspase-1 filaments nucleate specifically from the B-end of ASC filaments, and that the interdomain linker modulates bundle formation. The ASC isoform ASCb, with a four-residue linker, adopts a distinct architecture, correlating with reduced Caspase-1 activation efficiency. In ASC THP-1 cells, only wild-type ASC, not interface-disrupting mutants, restored ASC speck formation and Caspase-1 activation, underscoring the requirement for intact multitrack bundles. Cryo-electron tomography captures snapshots of higher-order inflammasome structures. These findings collectively define the structural and functional principles by which ASC organizes inflammasomes to amplify immune signaling.
History
DepositionSep 29, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66403.png

Downloads & links

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Map

FileDownload / File: emd_66403.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.091593534 - 0.2316217
Average (Standard dev.)0.002662367 (±0.015300213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66403_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66403_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66403_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Filament

EntireName: Filament
Components
  • Cell: Filament
    • Protein or peptide: Caspase-1

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Supramolecule #1: Filament

SupramoleculeName: Filament / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caspase-1

MacromoleculeName: Caspase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: caspase-1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.213551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADKVLKEKR KLFIRSMGEG TINGLLDELL QTRVLNKEEM EKVKRENATV MDKTRALIDS VIPKGAQACQ ICITYICEED SYLAGTLGL SADQTSGNYL NMQDSQGVLS SFPAPQAVQD NPAMPTSSGS EGNVKLCSLE EAQRIWKQKS AEIYPIMDKS S RTRLALII ...String:
MADKVLKEKR KLFIRSMGEG TINGLLDELL QTRVLNKEEM EKVKRENATV MDKTRALIDS VIPKGAQACQ ICITYICEED SYLAGTLGL SADQTSGNYL NMQDSQGVLS SFPAPQAVQD NPAMPTSSGS EGNVKLCSLE EAQRIWKQKS AEIYPIMDKS S RTRLALII CNEEFDSIPR RTGAEVDITG MTMLLQNLGY SVDVKKNLTA SDMTTELEAF AHRPEHKTSD STFLVFMSHG IR EGICGKK HSEQVPDILQ LNAIFNMLNT KNCPSLKDKP KVIIIQACRG DSPGVVWFKD SVGVSGNLSL PTTEEFEDDA IKK AHIEKD FIAFCSSTPD NVSWRHPTMG SVFIGRLIEH MQEYACSCDV EEIFRKVRFS FEQPDGRAQM PTTERVTLTR CFYL FPGH

UniProtKB: 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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.1 Å
Applied symmetry - Helical parameters - Δ&Phi: -100.2 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 194125
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9wz6

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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